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comparison shm_csr.xml @ 78:aff3ba86ef7a draft

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author davidvanzessen
date Mon, 31 Aug 2020 11:20:08 -0400
parents 58d2377b507d
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77:58d2377b507d 78:aff3ba86ef7a
1 <tool id="shm_csr" name="SHM &amp; CSR pipeline" version="1.0"> 1 <tool id="shm_csr" name="SHM &amp; CSR pipeline" version="1.0">
2 <description></description> 2 <description></description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.7">python</requirement> 4 <requirement type="package" version="2.7">python</requirement>
5 <requirement type="package" version="1.16.0">numpy</requirement>
5 <requirement type="package" version="1.2.0">xlrd</requirement> 6 <requirement type="package" version="1.2.0">xlrd</requirement>
6 <requirement type="package" version="3.0.0">r-ggplot2</requirement> 7 <requirement type="package" version="3.0.0">r-ggplot2</requirement>
7 <requirement type="package" version="1.4.3">r-reshape2</requirement> 8 <requirement type="package" version="1.4.3">r-reshape2</requirement>
8 <requirement type="package" version="0.5.0">r-scales</requirement> 9 <requirement type="package" version="0.5.0">r-scales</requirement>
9 <requirement type="package" version="3.4_5">r-seqinr</requirement> 10 <requirement type="package" version="3.4_5">r-seqinr</requirement>
10 <requirement type="package" version="1.11.4">r-data.table</requirement> 11 <requirement type="package" version="1.11.4">r-data.table</requirement>
11 <!--<requirement type="package" version="0.4.5">changeo</requirement>-->
12 </requirements> 12 </requirements>
13 <command interpreter="bash"> 13 <command interpreter="bash">
14 #if str ( $filter_unique.filter_unique_select ) == "remove": 14 #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 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
16 #else: 16 #else: