Mercurial > repos > davidvanzessen > shm_csr

comparison shm_csr.xml @ 83:729738462297 draft

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"planemo upload commit c0ffc68aec5836d5b20b543106493056a87edf57"
author rhpvorderman
date Wed, 15 Sep 2021 12:24:06 +0000
parents b6f9a640e098
children 4db34e32dd47
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82:a103134ee6e0 83:729738462297
1 <tool id="shm_csr" name="SHM &amp; CSR pipeline" version="1.0"> 1 <tool id="shm_csr" name="SHM &amp; CSR pipeline" version="1.1">
2 <description></description> 2 <description></description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.7">python</requirement> 4 <requirement type="package" version="3.7">python</requirement>
5 <requirement type="package" version="1.16.0">numpy</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.
7 Later versions of biopython break changeo 0.4.4 because of the Alphabet deprecation.-->
8 <requirement type="package" version="1.72">biopython</requirement>
6 <requirement type="package" version="1.2.0">xlrd</requirement> 9 <requirement type="package" version="1.2.0">xlrd</requirement>
7 <requirement type="package" version="3.0.0">r-ggplot2</requirement> 10 <requirement type="package" version="3.0.0">r-ggplot2</requirement>
8 <requirement type="package" version="1.4.3">r-reshape2</requirement> 11 <requirement type="package" version="1.4.3">r-reshape2</requirement>
9 <requirement type="package" version="0.5.0">r-scales</requirement> 12 <requirement type="package" version="0.5.0">r-scales</requirement>
10 <requirement type="package" version="3.4_5">r-seqinr</requirement> 13 <requirement type="package" version="3.4_5">r-seqinr</requirement>
11 <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>
16 <requirement type="package" version="4.4.18">bash</requirement>
17 <requirement type="package" version="1.34">tar</requirement>
18 <requirement type="package" version="5.39">file</requirement>
12 </requirements> 19 </requirements>
13 <command interpreter="bash"> 20 <command interpreter="bash">
14 #if str ( $filter_unique.filter_unique_select ) == "remove": 21 #if str ( $filter_unique.filter_unique_select ) == "remove":
15 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
16 #else: 23 #else: