comparison crossSampleOverview.xml @ 2:a64ece32a01a draft default tip

"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit a46097db0b6056e1125237393eb6974cfd51eb41"

1:bca68066a957

<tool id="cross_sample_overview" name="Generate overview information" version="1.1+galaxy0">
  <description>of a multi-sample analysis.</description>
  <requirements>
    <requirement type="package" version="2.0.2">ig-flowtools</requirement>
  </requirements>
  <stdio>
    <exit_code range="1" level="fatal" description="There are too many populations in the input files. The maximum number of populations is 40." />
    <exit_code range="2" level="fatal" description="There are populations inconsistencies between provided inputs." />
  </stdio>
  <command><![CDATA[
    mkdir templates &&
    mkdir -p static/flowtools &&
    mkdir -p static/images/flowtools &&
    export FLOWTOOL='which crossSampleOverview.py' &&
    FLOWTOOLDIR=\$(dirname $FLOWTOOL) &&
    cp $FLOWTOOLDIR/../share/templates/* templates/ &&
    cp -r $FLOWTOOLDIR/../share/static/flowtools/* static/flowtools/ &&
    cp $FLOWTOOLDIR/../share/static/images/flowtools/* static/images/flowtools/ &&
    crossSampleOverview.py -i '${input}' -I '${inputmfi}' -o '${html_file}' -m '${mfi}' -d '${html_file.files_path}' -t 'templates/'
    #for $f in $cs_outputs
       -s $f
    #end for
  ]]>
  </command>
  <inputs>
    <param format="flowstat1" name="input" type="data" label="CrossSample Population Summary Table"/>
    <param format="flowstat2" name="inputmfi" type="data" label="Centroids MFI Summary Table"/>

        </collection>
      </param>
      <output name="html_file" file="out.html" compare="sim_size">
        <extra_files type="file" name="csAllMFIs.tsv" value="csAllMFIs.tsv"/>
        <extra_files type="file" name="csOverview.tsv" value="csOverview.tsv"/>
        <extra_files type="file" name="csBoxplotData.json" value="csBoxplotData.json" compare="contains"/>
      </output>
    </test>
  </tests>
  <help><![CDATA[
   This tool generates an overview of the flow analysis results.

2:a64ece32a01a

<tool id="cross_sample_overview" name="Generate overview information" version="1.1+galaxy1">
  <description>of a multi-sample analysis.</description>
  <requirements>
    <requirement type="package" version="1.0.5">pandas</requirement>
    <requirement type="package" version="2.11.2">jinja2</requirement>
  </requirements>
  <stdio>
    <exit_code range="1" level="fatal" description="There are too many populations in the input files. The maximum number of populations is 40." />
    <exit_code range="2" level="fatal" description="There are populations inconsistencies between provided inputs." />
    <exit_code range="3:"/>
  </stdio>
  <command><![CDATA[
    python '$__tool_directory__/crossSampleOverview.py' -i '${input}' -I '${inputmfi}' -o '${html_file}' -m '${mfi}' -d '${html_file.files_path}' -t '$__tool_directory__'
    #for $f in $cs_outputs
       -s $f
    #end for
    ;
    cp -r '$__tool_directory__'/js '${html_file.files_path}/';
    cp -r '$__tool_directory__'/css '${html_file.files_path}/';
    cp -r '$__tool_directory__'/images '${html_file.files_path}/';
  ]]>
  </command>
  <inputs>
    <param format="flowstat1" name="input" type="data" label="CrossSample Population Summary Table"/>
    <param format="flowstat2" name="inputmfi" type="data" label="Centroids MFI Summary Table"/>

        </collection>
      </param>
      <output name="html_file" file="out.html" compare="sim_size">
        <extra_files type="file" name="csAllMFIs.tsv" value="csAllMFIs.tsv"/>
        <extra_files type="file" name="csOverview.tsv" value="csOverview.tsv"/>
        <extra_files type="file" name="csBoxplotData.json" value="csBoxplotData.json" compare="sim_size"/>
      </output>
    </test>
  </tests>
  <help><![CDATA[
   This tool generates an overview of the flow analysis results.