Mercurial > repos > immport-devteam > cs_overview

comparison crossSampleOverview.xml @ 2:a64ece32a01a draft default tip

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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/cs_overview commit a46097db0b6056e1125237393eb6974cfd51eb41"
author azomics
date Tue, 28 Jul 2020 08:32:36 -0400
parents bca68066a957
children
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1:bca68066a957 2:a64ece32a01a
1 <tool id="cross_sample_overview" name="Generate overview information" version="1.1+galaxy0"> 1 <tool id="cross_sample_overview" name="Generate overview information" version="1.1+galaxy1">
2 <description>of a multi-sample analysis.</description> 2 <description>of a multi-sample analysis.</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.0.2">ig-flowtools</requirement> 4 <requirement type="package" version="1.0.5">pandas</requirement>
5 <requirement type="package" version="2.11.2">jinja2</requirement>
5 </requirements> 6 </requirements>
6 <stdio> 7 <stdio>
7 <exit_code range="1" level="fatal" description="There are too many populations in the input files. The maximum number of populations is 40." /> 8 <exit_code range="1" level="fatal" description="There are too many populations in the input files. The maximum number of populations is 40." />
8 <exit_code range="2" level="fatal" description="There are populations inconsistencies between provided inputs." /> 9 <exit_code range="2" level="fatal" description="There are populations inconsistencies between provided inputs." />
10 <exit_code range="3:"/>
9 </stdio> 11 </stdio>
10 <command><![CDATA[ 12 <command><![CDATA[
11 mkdir templates && 13 python '$__tool_directory__/crossSampleOverview.py' -i '${input}' -I '${inputmfi}' -o '${html_file}' -m '${mfi}' -d '${html_file.files_path}' -t '$__tool_directory__'
12 mkdir -p static/flowtools &&
13 mkdir -p static/images/flowtools &&
14 export FLOWTOOL='which crossSampleOverview.py' &&
15 FLOWTOOLDIR=\$(dirname $FLOWTOOL) &&
16 cp $FLOWTOOLDIR/../share/templates/* templates/ &&
17 cp -r $FLOWTOOLDIR/../share/static/flowtools/* static/flowtools/ &&
18 cp $FLOWTOOLDIR/../share/static/images/flowtools/* static/images/flowtools/ &&
19 crossSampleOverview.py -i '${input}' -I '${inputmfi}' -o '${html_file}' -m '${mfi}' -d '${html_file.files_path}' -t 'templates/'
20 #for $f in $cs_outputs 14 #for $f in $cs_outputs
21 -s $f 15 -s $f
22 #end for 16 #end for
17 ;
18 cp -r '$__tool_directory__'/js '${html_file.files_path}/';
19 cp -r '$__tool_directory__'/css '${html_file.files_path}/';
20 cp -r '$__tool_directory__'/images '${html_file.files_path}/';
23 ]]> 21 ]]>
24 </command> 22 </command>
25 <inputs> 23 <inputs>
26 <param format="flowstat1" name="input" type="data" label="CrossSample Population Summary Table"/> 24 <param format="flowstat1" name="input" type="data" label="CrossSample Population Summary Table"/>
27 <param format="flowstat2" name="inputmfi" type="data" label="Centroids MFI Summary Table"/> 25 <param format="flowstat2" name="inputmfi" type="data" label="Centroids MFI Summary Table"/>
45 </collection> 43 </collection>
46 </param> 44 </param>
47 <output name="html_file" file="out.html" compare="sim_size"> 45 <output name="html_file" file="out.html" compare="sim_size">
48 <extra_files type="file" name="csAllMFIs.tsv" value="csAllMFIs.tsv"/> 46 <extra_files type="file" name="csAllMFIs.tsv" value="csAllMFIs.tsv"/>
49 <extra_files type="file" name="csOverview.tsv" value="csOverview.tsv"/> 47 <extra_files type="file" name="csOverview.tsv" value="csOverview.tsv"/>
50 <extra_files type="file" name="csBoxplotData.json" value="csBoxplotData.json" compare="contains"/> 48 <extra_files type="file" name="csBoxplotData.json" value="csBoxplotData.json" compare="sim_size"/>
51 </output> 49 </output>
52 </test> 50 </test>
53 </tests> 51 </tests>
54 <help><![CDATA[ 52 <help><![CDATA[
55 This tool generates an overview of the flow analysis results. 53 This tool generates an overview of the flow analysis results.