Mercurial > repos > davidvanzessen > shm_csr

comparison shm_csr.xml @ 96:385dea3c6cb5 draft

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planemo upload commit 423a48569c69301fdbf893ac3a649128404dfff5
author rhpvorderman
date Fri, 05 Jan 2024 08:53:22 +0000
parents d63eff357515
children fbc6307dd83b
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95:d63eff357515 96:385dea3c6cb5
1 <tool id="shm_csr" name="SHM &amp; CSR pipeline" version="1.8.1" profile="16.04"> 1 <tool id="shm_csr" name="SHM &amp; CSR pipeline" version="1.9.0" 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.
22 </requirements> 22 </requirements>
23 <command interpreter="bash"> 23 <command interpreter="bash">
24 <![CDATA[ 24 <![CDATA[
25 #import os 25 #import os
26 #set $input=os.path.basename($in_file.name) 26 #set $input=os.path.basename($in_file.name)
27 ln -s "$in_file" "$input" &&
28 #if str ( $filter_unique.filter_unique_select ) == "remove": 27 #if str ( $filter_unique.filter_unique_select ) == "remove":
29 $__tool_directory__/wrapper.sh "$input" 28 $__tool_directory__/wrapper.sh "$in_file"
30 custom $out_file $out_file.files_path 29 custom $out_file $out_file.files_path
31 "$input" "-" $functionality $unique 30 "$input" "-" $functionality $unique
32 $naive_output_cond.naive_output $naive_output_ca $naive_output_cg 31 $naive_output_cond.naive_output $naive_output_ca $naive_output_cg
33 $naive_output_cm $naive_output_ce $naive_output_all $naive_output_igm_naive 32 $naive_output_cm $naive_output_ce $naive_output_all $naive_output_igm_naive
34 $naive_output_igm_naive_memory 33 $naive_output_igm_naive_memory
58 <param name="empty_region_filter" type="select" label="Sequence starts at" help="" > 57 <param name="empty_region_filter" type="select" label="Sequence starts at" help="" >
59 <option value="leader" selected="true">Leader: include FR1, CDR1, FR2, CDR2, FR3 in filters</option> 58 <option value="leader" selected="true">Leader: include FR1, CDR1, FR2, CDR2, FR3 in filters</option>
60 <option value="FR1" selected="true">FR1: include CDR1,FR2,CDR2,FR3 in filters</option> 59 <option value="FR1" selected="true">FR1: include CDR1,FR2,CDR2,FR3 in filters</option>
61 <option value="CDR1">CDR1: include FR2,CDR2,FR3 in filters</option> 60 <option value="CDR1">CDR1: include FR2,CDR2,FR3 in filters</option>
62 <option value="FR2">FR2: include CDR2,FR3 in filters</option> 61 <option value="FR2">FR2: include CDR2,FR3 in filters</option>
62 <option value="None">No filter: sequences with mission regions are not filtered.</option>
63 </param> 63 </param>
64 <param name="functionality" type="select" label="Functionality filter" help="" > 64 <param name="functionality" type="select" label="Functionality filter" help="" >
65 <option value="productive" selected="true">Productive (Productive and Productive see comment)</option> 65 <option value="productive" selected="true">Productive (Productive and Productive see comment)</option>
66 <option value="unproductive">Unproductive (Unproductive and Unproductive see comment)</option> 66 <option value="unproductive">Unproductive (Unproductive and Unproductive see comment)</option>
67 <option value="remove_unknown">Productive and Unproductive (Productive, Productive see comment, Unproductive, Unproductive and Unproductive see comment)</option> 67 <option value="remove_unknown">Productive and Unproductive (Productive, Productive see comment, Unproductive, Unproductive and Unproductive see comment)</option>