diff galaxy-tools/biobank/tools/flowcell_samplesheet.xml @ 0:ba6cf6ede027 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy-tools/biobank/tools/flowcell_samplesheet.xml	Wed Sep 28 06:03:30 2016 -0400
@@ -0,0 +1,107 @@
+<tool id="vl_tools_flowcell_samplesheet" name="VLT.flowcell_samplesheet">
+  <description>
+    Build the samplesheet for a given FlowCell
+  </description>
+
+  <command interpreter="bash">
+    launcher.sh
+    --interpreter=python
+    --runner=kb_query.py
+    --host=$__user_omero_host__
+    --user=$__user_omero_user__
+    --passwd=$__user_omero_password__
+    --operator=$__user_email__
+    --loglevel=$__app__.config.vl_loglevel
+    --logfile=${logfile}
+    --ofile=${outfile}
+    flowcell_samplesheet
+    #if $namespace.ignore_namespace
+      --flowcell=${flowcell}
+      --ignore_namespace
+    #else
+      --flowcell="${namespace.namespace_value}|${flowcell}"
+    #end if
+    #if $remove_namespaces
+      --remove_namespaces
+    #end if
+    #if $add_sample_label
+      --sample_label
+    #end if
+    --separator=${csv_separator}
+  </command>
+
+  <inputs>
+    <param name="flowcell" type="text" size="30"
+	   label="Flowcell ID" optional="false"
+	   help="Flowcell ID (with or without a leading namespace)"/>
+    <conditional name="namespace">
+      <param name="ignore_namespace" type="boolean" checked="true"
+	     label="Ignore Flowcell ID namespace"
+	     help="Ignore namespace when searching the given Flowcell ID into Omero. NOTE well: if two or more Flowcells share the same ID (but were saved with different namespaces) the tool will generate an error"/>
+      <when value="false">
+	<param name="namespace_value" type="text" size="15"
+	       label="Namespace" optional="false"
+	       help="Namespace that will be used when looking for the specified Flowcell ID"/>
+      </when>
+    </conditional>
+    <param name="add_sample_label" type="boolean" checked="false"
+	   label="Add sample labels"
+	   help="Add the SampleLabel column and labels to each row in the output file"/>
+    <param name="remove_namespaces" type="boolean" checked="true"
+	   label="Remove namespaces"
+	   help="Remove namespaces for Flowcell and Samples in the output file"/>
+    <param name="csv_separator" type="select" label="Output file fields separator">
+      <option value=" ">Whitespaces</option>
+      <option value=".">Dots</option>
+      <option value="," selected="true">Commas</option>
+      <option value="-">Dashes</option>
+      <option value="_">Underscores</option>
+      <option value="|">Pipes</option>
+      <option value=":">Colons</option>
+    </param>
+
+    <!-- ************************************************** -->
+
+
+  </inputs>
+
+  <outputs>
+    <data format="txt" name="logfile" label="${tool.name}.log"/>
+    <data format="csv" name="outfile" label="${tool.name}.csv"/>
+  </outputs>
+
+  <stdio>
+    <exit_code range="1:" level="fatal" />
+  </stdio>
+
+  <help>
+
+Export data related to a FlowCell identified by the Flowcell ID field
+into a csv file like
+
+ FCID,Lane,SampleID,SampleRef,Index,Description,Control,Recipe,Operator
+
+ foofc1,1,v012aa2,hg19,ATCACG,,WG,john doe
+
+ foofc1,2,v0441a1,hg19,GATCAG,,EXOME,john doe
+
+ foofc1,2,v021441,hg19,TAGCTT,,WG,john doe
+
+ ...
+
+If the checkbox "Add sample labels" is enabled, the output file will
+have a new column at the end of each row with the Label of the sample
+like
+
+ FCID,Lane,SampleID,SampleRef,Index,Description,Control,Recipe,Operator,SampleLabel
+
+ foofc1,1,v012aa2,hg19,ATCACG,,WG,john doe,foosmp1
+
+ foofc1,2,v0441a1,hg19,GATCAG,,EXOME,john doe,foosmp2
+
+ foofc1,2,v021441,hg19,TAGCTT,,WG,john doe,foosmp3
+
+ ...
+
+  </help>
+</tool>
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