Mercurial > repos > davidvanzessen > shm_csr

comparison shm_csr.xml @ 84:4db34e32dd47 draft

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"planemo upload commit 78ace939ed7437b8b360588032449a99aad949eb"
author rhpvorderman
date Wed, 27 Oct 2021 09:38:20 +0000
parents 729738462297
children a539d14d66b6
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83:729738462297 84:4db34e32dd47
1 <tool id="shm_csr" name="SHM &amp; CSR pipeline" version="1.1"> 1 <tool id="shm_csr" name="SHM &amp; CSR pipeline" version="1.2">
2 <description></description> 2 <description></description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="3.7">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.-->
8 <requirement type="package" version="1.72">biopython</requirement> 8 <requirement type="package" version="1.72">biopython</requirement>
9 <requirement type="package" version="1.2.0">xlrd</requirement> 9 <requirement type="package" version="1.2.0">xlrd</requirement>
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>
19 </requirements> 20 </requirements>
20 <command interpreter="bash"> 21 <command interpreter="bash">
21 #if str ( $filter_unique.filter_unique_select ) == "remove": 22 #if str ( $filter_unique.filter_unique_select ) == "remove":
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 23 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
23 #else: 24 #else: