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

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<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>