correction to configurations and adding a test compressed archive

isaconfig-default_v2013-02-13/envgen_survey_seq.xml

@@ -1,6 +1,141 @@
-<isatab-config-file xmlns="http://www.ebi.ac.uk/bii/isatab_configuration#"><isatab-configuration table-name="envgen_survey_seq" isatab-assay-type="generic_assay" isatab-conversion-target="sra"><measurement term-label="environmental gene survey" term-accession="" source-abbreviation="OBI"/><technology term-label="nucleotide sequencing" term-accession="obo:OBI_0000626" source-abbreviation="OBI"/><field header="Sample Name" data-type="String" is-file-field="false" is-multiple-value="true" is-required="true" is-hidden="false" is-forced-ontology="false"><description><![CDATA[Samples represent major outputs resulting from a protocol application other than the special case outputs of Extract or a Labeled Extract.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT]
-            </generated-value-template></field><protocol-field protocol-type ="nucleic acid extraction"/><field header="Extract Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false" is-forced-ontology="false"><description><![CDATA[User-defined names for each portion of extracted material.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>
+<isatab-config-file xmlns="http://www.ebi.ac.uk/bii/isatab_configuration#">
+    <isatab-configuration table-name="envgen_survey_seq" isatab-assay-type="generic_assay"
+        isatab-conversion-target="sra">
+        <measurement term-label="environmental gene survey" term-accession=""
+            source-abbreviation="OBI"/>
+        <technology term-label="nucleotide sequencing" term-accession="obo:OBI_0000626"
+            source-abbreviation="OBI"/>
+        <field header="Sample Name" data-type="String" is-file-field="false"
+            is-multiple-value="true" is-required="true" is-hidden="false" is-forced-ontology="false">
+            <description><![CDATA[Samples represent major outputs resulting from a protocol application other than the special case outputs of Extract or a Labeled Extract.]]></description>
+            <default-value><![CDATA[]]></default-value>
+            <generated-value-template>[INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT]
+            </generated-value-template>
+        </field>
+        <protocol-field protocol-type="nucleic acid extraction"/>
+        <field header="Extract Name" data-type="String" is-file-field="false"
+            is-multiple-value="false" is-required="true" is-hidden="false"
+            is-forced-ontology="false">
+            <description><![CDATA[User-defined names for each portion of extracted material.]]></description>
+            <default-value><![CDATA[]]></default-value>
+            <generated-value-template>
                 [INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT].Extract-[EXTRACT_COUNT]
-            </generated-value-template></field><protocol-field protocol-type ="library construction"/><field header="Parameter Value[target_taxon]" data-type="List" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false" is-forced-ontology="false"><description><![CDATA[provide the taxonomic group targeted by this survey. for instance Archae, Bacteria, Eukaryota]]></description><default-value><![CDATA[]]></default-value><list-values>Archeae,Bacteria,Eukaryota</list-values></field><field header="Parameter Value[target_gene]" data-type="List" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false" is-forced-ontology="false"><description><![CDATA[In Environmental Gene Survey Studies, report the gene of interest used to monitor diversity]]></description><default-value><![CDATA[]]></default-value><list-values>16S rRNA,18S rRNA,RBCL,matK,COX1,ITS1-5.8S-ITS2</list-values></field><field header="Parameter Value[target_subfragment]" data-type="List" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false" is-forced-ontology="false"><description><![CDATA[In Environmental Gene Survey Studies, depends on declaring a target_gene, allows added specificity]]></description><default-value><![CDATA[]]></default-value><list-values>V6,V9,ITS</list-values></field><field header="Parameter Value[pcr_primers]" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false" is-forced-ontology="false"><description><![CDATA[In Environmental Gene Survey Studies, mandatory information, formatting according to miens specifications]]></description><default-value><![CDATA[]]></default-value></field><field header="Parameter Value[pcr_cond]" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false" is-forced-ontology="false"><description><![CDATA[In Environmental Gene Survey Studies, mandatory information, formatting according to miens specifications]]></description><default-value><![CDATA[]]></default-value></field><field header="Parameter Value[mid]" data-type="String" is-file-field="false" is-multiple-value="true" is-required="false" is-hidden="false" is-forced-ontology="false"><description><![CDATA['mid' stands for 'multiplex identifier' (aka barcode tag). Use this field when performing a multiplexing procedure and indicate here the nucleic acid tag used to uniquely identify the sample if the pool.]]></description><default-value><![CDATA[]]></default-value></field><field header="Parameter Value[library layout]" data-type="List" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false" is-forced-ontology="false"><description><![CDATA[specifies whether to expect single, paired, or other configuration of reads.(SRA 1.2 documentation)]]></description><default-value><![CDATA[]]></default-value><list-values>SINGLE,PAIRED</list-values></field><protocol-field protocol-type ="nucleic acid sequencing"/><field header="Parameter Value[sequencing instrument]" data-type="List" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false" is-forced-ontology="false"><description><![CDATA[a parameter to report the sequencing instrument model and make]]></description><default-value><![CDATA[]]></default-value><list-values>454 GS,454 GS 20,454 GS FLX,454 GS FLX Plus,454 GS FLX Titanium,454 GS Junior,AB SOLiD System,AB SOLiD System 2.0,AB SOLiD System 3.0,AB SOLiD 4 System,AB SOLiD 4hq System,AB SOLiD PI System,AB SOLiD 5500,AB SOLiD 5500xl,AB 5500 Genetic Analyzer,AB 5500xl Genetic analyzer,Illumina Genome Analyzer,Illumina Genome Analyzer II,Illumina Genome Analyzer IIx,Illumina HiSeq 1000,Illumina HiSeq 2000,Illumina HiSeq 2500,Illumina HiScanSQ,Illumina MiSeq,Ion Torrent PGM,Ion Torrent Proton,Sanger sequencing instrument,unspecified</list-values></field><field header="Parameter Value[quality scorer]" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false" is-forced-ontology="false"><description><![CDATA[Name and version of the quality scoring software.]]></description><default-value><![CDATA[]]></default-value></field><field header="Parameter Value[base caller]" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false" is-forced-ontology="false"><description><![CDATA[Name and version of the base or color calling software.]]></description><default-value><![CDATA[]]></default-value></field><field header="Assay Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="true" is-hidden="false" is-forced-ontology="false"><description><![CDATA[User-defined name for an assay.]]></description><default-value><![CDATA[]]></default-value><generated-value-template>
+            </generated-value-template>
+        </field>
+        <protocol-field protocol-type="library construction"/>
+        <field header="Parameter Value[target_taxon]" data-type="List" is-file-field="false"
+            is-multiple-value="false" is-required="false" is-hidden="false"
+            is-forced-ontology="false">
+            <description><![CDATA[provide the taxonomic group targeted by this survey. for instance Archae, Bacteria, Eukaryota]]></description>
+            <default-value><![CDATA[]]></default-value>
+            <list-values>Archeae,Bacteria,Eukaryota</list-values>
+        </field>
+        <field header="Parameter Value[target_gene]" data-type="List" is-file-field="false"
+            is-multiple-value="false" is-required="false" is-hidden="false"
+            is-forced-ontology="false">
+            <description><![CDATA[In Environmental Gene Survey Studies, report the gene of interest used to monitor diversity]]></description>
+            <default-value><![CDATA[]]></default-value>
+            <list-values>16S rRNA,18S rRNA,RBCL,matK,COX1,ITS1-5.8S-ITS2</list-values>
+        </field>
+        <field header="Parameter Value[target_subfragment]" data-type="List" is-file-field="false"
+            is-multiple-value="false" is-required="false" is-hidden="false"
+            is-forced-ontology="false">
+            <description><![CDATA[In Environmental Gene Survey Studies, depends on declaring a target_gene, allows added specificity]]></description>
+            <default-value><![CDATA[]]></default-value>
+            <list-values>V6,V9,ITS</list-values>
+        </field>
+        <field header="Parameter Value[pcr_primers]" data-type="String" is-file-field="false"
+            is-multiple-value="false" is-required="false" is-hidden="false"
+            is-forced-ontology="false">
+            <description><![CDATA[In Environmental Gene Survey Studies, mandatory information, formatting according to miens specifications]]></description>
+            <default-value><![CDATA[]]></default-value>
+        </field>
+        <field header="Parameter Value[pcr_cond]" data-type="String" is-file-field="false"
+            is-multiple-value="false" is-required="false" is-hidden="false"
+            is-forced-ontology="false">
+            <description><![CDATA[In Environmental Gene Survey Studies, mandatory information, formatting according to miens specifications]]></description>
+            <default-value><![CDATA[]]></default-value>
+        </field>
+        <field header="Parameter Value[mid]" data-type="String" is-file-field="false"
+            is-multiple-value="true" is-required="false" is-hidden="false"
+            is-forced-ontology="false">
+            <description><![CDATA['mid' stands for 'multiplex identifier' (aka barcode tag). Use this field when performing a multiplexing procedure and indicate here the nucleic acid tag used to uniquely identify the sample if the pool.]]></description>
+            <default-value><![CDATA[]]></default-value>
+        </field>
+        <field header="Parameter Value[library layout]" data-type="List" is-file-field="false"
+            is-multiple-value="false" is-required="false" is-hidden="false"
+            is-forced-ontology="false">
+            <description><![CDATA[specifies whether to expect single, paired, or other configuration of reads.(SRA 1.2 documentation)]]></description>
+            <default-value><![CDATA[]]></default-value>
+            <list-values>SINGLE,PAIRED</list-values>
+        </field>
+        <protocol-field protocol-type="nucleic acid sequencing"/>
+        <field header="Parameter Value[sequencing instrument]" data-type="List"
+            is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false"
+            is-forced-ontology="false">
+            <description><![CDATA[a parameter to report the sequencing instrument model and make]]></description>
+            <default-value><![CDATA[]]></default-value>
+            <list-values>454 GS,454 GS 20,454 GS FLX,454 GS FLX Plus,454 GS FLX Titanium,454 GS
+                Junior,AB SOLiD System,AB SOLiD System 2.0,AB SOLiD System 3.0,AB SOLiD 4 System,AB
+                SOLiD 4hq System,AB SOLiD PI System,AB SOLiD 5500,AB SOLiD 5500xl,AB 5500 Genetic
+                Analyzer,AB 5500xl Genetic analyzer,Illumina Genome Analyzer,Illumina Genome
+                Analyzer II,Illumina Genome Analyzer IIx,Illumina HiSeq 1000,Illumina HiSeq
+                2000,Illumina HiSeq 2500,Illumina HiScanSQ,Illumina MiSeq,Ion Torrent PGM,Ion
+                Torrent Proton,Sanger sequencing instrument,unspecified</list-values>
+        </field>
+        <field header="Parameter Value[quality scorer]" data-type="String" is-file-field="false"
+            is-multiple-value="false" is-required="false" is-hidden="false"
+            is-forced-ontology="false">
+            <description><![CDATA[Name and version of the quality scoring software.]]></description>
+            <default-value><![CDATA[]]></default-value>
+        </field>
+        <field header="Parameter Value[base caller]" data-type="String" is-file-field="false"
+            is-multiple-value="false" is-required="false" is-hidden="false"
+            is-forced-ontology="false">
+            <description><![CDATA[Name and version of the base or color calling software.]]></description>
+            <default-value><![CDATA[]]></default-value>
+        </field>
+        <field header="Assay Name" data-type="String" is-file-field="false"
+            is-multiple-value="false" is-required="true" is-hidden="false"
+            is-forced-ontology="false">
+            <description><![CDATA[User-defined name for an assay.]]></description>
+            <default-value><![CDATA[]]></default-value>
+            <generated-value-template>
                 [INSTITUTION].Group-[GROUP_NO].Subject-[SUBJECT_NO].[SAMPLE_EXTRACT].Extract-[EXTRACT_COUNT].LE-[LABEL_COUNT].ASSAY-[HYB_COUNT]
-            </generated-value-template></field><field header="Comment[Export]" data-type="List" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false" is-forced-ontology="false"><description><![CDATA[Use this field to select/set which records should be exported for a submission to SRA/ENA]]></description><default-value><![CDATA[no]]></default-value><list-values>yes,no</list-values></field><field header="Raw Data File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="true" is-hidden="false" is-forced-ontology="false"><description><![CDATA[Name (or URI) of the raw data file generated by an assay.]]></description><default-value><![CDATA[]]></default-value></field><protocol-field protocol-type ="sequence analysis data transformation"/><field header="Normalization Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false" is-forced-ontology="false"><description><![CDATA[User-defined name for each normalization applied]]></description><default-value><![CDATA[]]></default-value></field><field header="Data Transformation Name" data-type="String" is-file-field="false" is-multiple-value="false" is-required="false" is-hidden="false" is-forced-ontology="false"><description><![CDATA[User-defined name for each data transformation applied]]></description><default-value><![CDATA[]]></default-value></field><field header="Derived Data File" data-type="String" is-file-field="true" is-multiple-value="false" is-required="false" is-hidden="false" is-forced-ontology="false"><description><![CDATA[Name (or URI) of the data file generated by an assay]]></description><default-value><![CDATA[]]></default-value></field><structured-field name="factors"/></isatab-configuration></isatab-config-file>
+            </generated-value-template>
+        </field>
+        <field header="Comment[Export]" data-type="List" is-file-field="false"
+            is-multiple-value="false" is-required="false" is-hidden="false"
+            is-forced-ontology="false">
+            <description><![CDATA[Use this field to select/set which records should be exported for a submission to SRA/ENA]]></description>
+            <default-value><![CDATA[no]]></default-value>
+            <list-values>yes,no</list-values>
+        </field>
+        <field header="Raw Data File" data-type="String" is-file-field="true"
+            is-multiple-value="false" is-required="true" is-hidden="false"
+            is-forced-ontology="false">
+            <description><![CDATA[Name (or URI) of the raw data file generated by an assay.]]></description>
+            <default-value><![CDATA[]]></default-value>
+        </field>
+        <protocol-field protocol-type="sequence analysis data transformation"/>
+        <field header="Normalization Name" data-type="String" is-file-field="false"
+            is-multiple-value="false" is-required="false" is-hidden="false"
+            is-forced-ontology="false">
+            <description><![CDATA[User-defined name for each normalization applied]]></description>
+            <default-value><![CDATA[]]></default-value>
+        </field>
+        <field header="Data Transformation Name" data-type="String" is-file-field="false"
+            is-multiple-value="false" is-required="false" is-hidden="false"
+            is-forced-ontology="false">
+            <description><![CDATA[User-defined name for each data transformation applied]]></description>
+            <default-value><![CDATA[]]></default-value>
+        </field>
+        <field header="Derived Data File" data-type="String" is-file-field="true"
+            is-multiple-value="false" is-required="false" is-hidden="false"
+            is-forced-ontology="false">
+            <description><![CDATA[Name (or URI) of the data file generated by an assay]]></description>
+            <default-value><![CDATA[]]></default-value>
+        </field>
+        <structured-field name="factors"/>
+    </isatab-configuration>
+</isatab-config-file>