Mercurial > repos > davidvanzessen > shm_csr

comparison shm_csr.xml @ 95:d63eff357515 draft

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planemo upload commit d96a736dcd6da34137f79861fbc6369716c332f1
author rhpvorderman
date Mon, 27 Mar 2023 13:11:53 +0000
parents 84e9e5c8c101
children 385dea3c6cb5
comparison
equal deleted inserted replaced
94:84e9e5c8c101 95:d63eff357515
1 <tool id="shm_csr" name="SHM &amp; CSR pipeline" version="1.8.0" profile="16.04"> 1 <tool id="shm_csr" name="SHM &amp; CSR pipeline" version="1.8.1" profile="16.04">
2 <description></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.
20 <requirement type="package" version="1.07.1">bc</requirement> 20 <requirement type="package" version="1.07.1">bc</requirement>
21 <requirement type="package" version="0.83">font-ttf-ubuntu</requirement> 21 <requirement type="package" version="0.83">font-ttf-ubuntu</requirement>
22 </requirements> 22 </requirements>
23 <command interpreter="bash"> 23 <command interpreter="bash">
24 <![CDATA[ 24 <![CDATA[
25 #set $input=$in_file.name 25 #import os
26 #set $input=os.path.basename($in_file.name)
26 ln -s "$in_file" "$input" && 27 ln -s "$in_file" "$input" &&
27 #if str ( $filter_unique.filter_unique_select ) == "remove": 28 #if str ( $filter_unique.filter_unique_select ) == "remove":
28 $__tool_directory__/wrapper.sh "$input" 29 $__tool_directory__/wrapper.sh "$input"
29 custom $out_file $out_file.files_path 30 custom $out_file $out_file.files_path
30 "${in_file.name}" "-" $functionality $unique 31 "$input" "-" $functionality $unique
31 $naive_output_cond.naive_output $naive_output_ca $naive_output_cg 32 $naive_output_cond.naive_output $naive_output_ca $naive_output_cg
32 $naive_output_cm $naive_output_ce $naive_output_all $naive_output_igm_naive 33 $naive_output_cm $naive_output_ce $naive_output_all $naive_output_igm_naive
33 $naive_output_igm_naive_memory 34 $naive_output_igm_naive_memory
34 $filter_unique.filter_unique_select 35 $filter_unique.filter_unique_select
35 $filter_unique.filter_unique_clone_count 36 $filter_unique.filter_unique_clone_count
144 <filter>class_filter_cond['class_filter'] != "101_101"</filter> 145 <filter>class_filter_cond['class_filter'] != "101_101"</filter>
145 <filter>class_filter_cond['class_filter'] != "101_101_IGA"</filter> 146 <filter>class_filter_cond['class_filter'] != "101_101_IGA"</filter>
146 <filter>class_filter_cond['class_filter'] != "101_101_IGG"</filter> 147 <filter>class_filter_cond['class_filter'] != "101_101_IGG"</filter>
147 <filter>class_filter_cond['class_filter'] != "101_101_IGM"</filter> 148 <filter>class_filter_cond['class_filter'] != "101_101_IGM"</filter>
148 </data> 149 </data>
149 <data format="imgt archive" name="naive_output_igm_naive" label = "Filtered naive IGM sequences (mutations below 2%): ${in_file.name}"> 150 <data format="imgt_archive" name="naive_output_igm_naive" label = "Filtered naive IGM sequences (mutations below 2%): ${in_file.name}">
150 <filter>naive_output_cond['naive_output'] == "yes"</filter> 151 <filter>naive_output_cond['naive_output'] == "yes"</filter>
151 <filter>class_filter_cond['class_filter'] != "101_101"</filter> 152 <filter>class_filter_cond['class_filter'] != "101_101"</filter>
152 <filter>class_filter_cond['class_filter'] != "101_101_IGA"</filter> 153 <filter>class_filter_cond['class_filter'] != "101_101_IGA"</filter>
153 <filter>class_filter_cond['class_filter'] != "101_101_IGG"</filter> 154 <filter>class_filter_cond['class_filter'] != "101_101_IGG"</filter>
154 </data> 155 </data>
155 <data format="imgt archive" name="naive_output_igm_naive_memory" label = "Filtered naive memory IGM sequences (mutations over 2%): ${in_file.name}"> 156 <data format="imgt_archive" name="naive_output_igm_naive_memory" label = "Filtered naive memory IGM sequences (mutations over 2%): ${in_file.name}">
156 <filter>naive_output_cond['naive_output'] == "yes"</filter> 157 <filter>naive_output_cond['naive_output'] == "yes"</filter>
157 <filter>class_filter_cond['class_filter'] != "101_101"</filter> 158 <filter>class_filter_cond['class_filter'] != "101_101"</filter>
158 <filter>class_filter_cond['class_filter'] != "101_101_IGA"</filter> 159 <filter>class_filter_cond['class_filter'] != "101_101_IGA"</filter>
159 <filter>class_filter_cond['class_filter'] != "101_101_IGG"</filter> 160 <filter>class_filter_cond['class_filter'] != "101_101_IGG"</filter>
160 </data> 161 </data>