Mercurial > repos > davidvanzessen > shm_csr

comparison shm_csr.xml @ 89:3c9d4d976c47 draft

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"planemo upload commit 8b702d0cf8f2355307eb8f95989f3d2488b2c963"
author rhpvorderman
date Fri, 05 Nov 2021 13:41:03 +0000
parents a84ac3ee87e1
children 6809c63d9161
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88:a84ac3ee87e1 89:3c9d4d976c47
1 <tool id="shm_csr" name="SHM &amp; CSR pipeline" version="1.2.1"> 1 <tool id="shm_csr" name="SHM &amp; CSR pipeline" version="1.3.0">
2 <description>Performs a summary/analysis of an IMGT HighV-QUEST (https://www.imgt.org/HighV-QUEST/) ZIP file for Somatic hypermutation and class switch recombination.</description> 2 <description></description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="3.7.1">python</requirement> 4 <requirement type="package" version="3.7.1">python</requirement>
5 <requirement type="package" version="0.4.4">changeo</requirement> 5 <requirement type="package" version="0.4.4">changeo</requirement>
6 <!--Biopython should be set at a version at the release of changeo 0.4.4. 6 <!--Biopython should be set at a version at the release of changeo 0.4.4.
7 Later versions of biopython break changeo 0.4.4 because of the Alphabet deprecation.--> 7 Later versions of biopython break changeo 0.4.4 because of the Alphabet deprecation.-->
14 <requirement type="package" version="1.11.4">r-data.table</requirement> 14 <requirement type="package" version="1.11.4">r-data.table</requirement>
15 <requirement type="package" version="6.0">unzip</requirement> 15 <requirement type="package" version="6.0">unzip</requirement>
16 <requirement type="package" version="4.4.18">bash</requirement> 16 <requirement type="package" version="4.4.18">bash</requirement>
17 <requirement type="package" version="1.34">tar</requirement> 17 <requirement type="package" version="1.34">tar</requirement>
18 <requirement type="package" version="5.39">file</requirement> 18 <requirement type="package" version="5.39">file</requirement>
19 <container type="docker">quay.io/rhpvorderman/mulled-v2-a2524529ff4c0254c944ff4606e926ca2e8b80d0:9fa3e7fda79c80bf1af596872bddd871913a2c1c-0</container>
20 <container type="singularity">docker://quay.io/rhpvorderman/mulled-v2-a2524529ff4c0254c944ff4606e926ca2e8b80d0:9fa3e7fda79c80bf1af596872bddd871913a2c1c-0</container>
21 </requirements> 19 </requirements>
22 <command interpreter="bash"> 20 <command interpreter="bash">
23 #if str ( $filter_unique.filter_unique_select ) == "remove": 21 #if str ( $filter_unique.filter_unique_select ) == "remove":
24 wrapper.sh $in_file custom $out_file $out_file.files_path "${in_file.name}" "-" $functionality $unique $naive_output_cond.naive_output $naive_output_ca $naive_output_cg $naive_output_cm $naive_output_ce $naive_output_all $filter_unique.filter_unique_select $filter_unique.filter_unique_clone_count $class_filter_cond.class_filter $empty_region_filter $fast 22 wrapper.sh $in_file custom $out_file $out_file.files_path "${in_file.name}" "-" $functionality $unique $naive_output_cond.naive_output $naive_output_ca $naive_output_cg $naive_output_cm $naive_output_ce $naive_output_all $filter_unique.filter_unique_select $filter_unique.filter_unique_clone_count $class_filter_cond.class_filter $empty_region_filter $fast
25 #else: 23 #else: