Mercurial > repos > davidvanzessen > shm_csr

comparison shm_csr.xml @ 93:8fcf31272f6e draft

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planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c
author rhpvorderman
date Mon, 06 Mar 2023 11:36:32 +0000
parents cf8ad181628f
children 84e9e5c8c101
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92:cf8ad181628f 93:8fcf31272f6e
1 <tool id="shm_csr" name="SHM &amp; CSR pipeline" version="1.6.0"> 1 <tool id="shm_csr" name="SHM &amp; CSR pipeline" version="1.7.0" 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.
19 <requirement type="package" version="4.6.0">findutils</requirement> 19 <requirement type="package" version="4.6.0">findutils</requirement>
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[
25 #set $input=$in_file.name
26 ln -s "$in_file" "$input" &&
24 #if str ( $filter_unique.filter_unique_select ) == "remove": 27 #if str ( $filter_unique.filter_unique_select ) == "remove":
25 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 28 $__tool_directory__/wrapper.sh "$input"
29 custom $out_file $out_file.files_path
30 "${in_file.name}" "-" $functionality $unique
31 $naive_output_cond.naive_output $naive_output_ca
32 $naive_output_cg $naive_output_cm $naive_output_ce
33 $naive_output_all $filter_unique.filter_unique_select
34 $filter_unique.filter_unique_clone_count
35 $class_filter_cond.class_filter
36 $empty_region_filter
37 $fast
26 #else: 38 #else:
27 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 2 $class_filter_cond.class_filter $empty_region_filter $fast 39 $__tool_directory__/wrapper.sh
40 "$input" custom
41 $out_file $out_file.files_path
42 "${in_file.name}" "-" $functionality $unique
43 $naive_output_cond.naive_output $naive_output_ca $naive_output_cg
44 $naive_output_cm $naive_output_ce $naive_output_all
45 $filter_unique.filter_unique_select
46 2
47 $class_filter_cond.class_filter
48 $empty_region_filter
49 $fast
28 #end if 50 #end if
51 ]]>
29 </command> 52 </command>
30 <inputs> 53 <inputs>
31 <param name="in_file" type="data" format="data" label="IMGT zip file to be analysed" /> 54 <param name="in_file" type="data" format="data" label="IMGT zip file to be analysed" />
32 <param name="empty_region_filter" type="select" label="Sequence starts at" help="" > 55 <param name="empty_region_filter" type="select" label="Sequence starts at" help="" >
33 <option value="leader" selected="true">Leader: include FR1, CDR1, FR2, CDR2, FR3 in filters</option> 56 <option value="leader" selected="true">Leader: include FR1, CDR1, FR2, CDR2, FR3 in filters</option>
54 <when value="no"></when> 77 <when value="no"></when>
55 </conditional> 78 </conditional>
56 <param name="unique" type="select" label="Remove duplicates based on" help="" > 79 <param name="unique" type="select" label="Remove duplicates based on" help="" >
57 <option value="VGene,CDR3.IMGT.AA,best_match_class">Top.V.Gene, CDR3 (AA), C region</option> 80 <option value="VGene,CDR3.IMGT.AA,best_match_class">Top.V.Gene, CDR3 (AA), C region</option>
58 <option value="VGene,CDR3.IMGT.AA">Top.V.Gene, CDR3 (AA)</option> 81 <option value="VGene,CDR3.IMGT.AA">Top.V.Gene, CDR3 (AA)</option>
82 <option value="VGene,JGene,CDR3.IMGT.AA">Top.V.Gene, Top.J.Gene, CDR3 (AA)</option>
59 <option value="CDR3.IMGT.AA,best_match_class">CDR3 (AA), C region</option> 83 <option value="CDR3.IMGT.AA,best_match_class">CDR3 (AA), C region</option>
60 <option value="CDR3.IMGT.AA">CDR3 (AA)</option> 84 <option value="CDR3.IMGT.AA">CDR3 (AA)</option>
61 85
62 <option value="VGene,CDR3.IMGT.seq,best_match_class">Top.V.Gene, CDR3 (nt), C region</option> 86 <option value="VGene,CDR3.IMGT.seq,best_match_class">Top.V.Gene, CDR3 (nt), C region</option>
63 <option value="VGene,CDR3.IMGT.seq">Top.V.Gene, CDR3 (nt)</option> 87 <option value="VGene,CDR3.IMGT.seq">Top.V.Gene, CDR3 (nt)</option>
88 <option value="VGene,JGene,CDR3.IMGT.seq">Top.V.Gene, Top.J.Gene, CDR3 (nt)</option>
64 <option value="CDR3.IMGT.seq,best_match_class">CDR3 (nt), C region</option> 89 <option value="CDR3.IMGT.seq,best_match_class">CDR3 (nt), C region</option>
65 <option value="CDR3.IMGT.seq">CDR3 (nt)</option> 90 <option value="CDR3.IMGT.seq">CDR3 (nt)</option>
91 <option value="VGene,DGene,JGene,CDR3.IMGT.seq">Top.V.Gene, Top.D.Gene, Top.J.Gene, CDR3 (nt)</option>
66 <option value="Sequence.ID" selected="true">Don't remove duplicates</option> 92 <option value="Sequence.ID" selected="true">Don't remove duplicates</option>
67 </param> 93 </param>
68 <conditional name="class_filter_cond"> 94 <conditional name="class_filter_cond">
69 <param name="class_filter" type="select" label="Human Class/Subclass filter" help="" > 95 <param name="class_filter" type="select" label="Human Class/Subclass filter" help="" >
70 <option value="70_70" selected="true">>70% class and >70% subclass</option> 96 <option value="70_70" selected="true">>70% class and >70% subclass</option>
71 <option value="60_55">>60% class and >55% subclass</option> 97 <option value="60_55">>60% class and >55% subclass</option>
72 <option value="70_0">>70% class</option> 98 <option value="70_0">>70% class</option>
73 <option value="60_0">>60% class</option> 99 <option value="60_0">>60% class</option>
74 <option value="19_0">>19% class</option> 100 <option value="19_0">>19% class</option>
75 <option value="101_101">Do not assign (sub)class</option> 101 <option value="101_101_all">Do not assign (sub)class</option>
102 <option value="101_101_IGM">Everything is IGM</option>
76 </param> 103 </param>
77 <when value="70_70"></when>
78 <when value="60_55"></when>
79 <when value="70_0"></when>
80 <when value="60_0"></when>
81 <when value="19_0"></when>
82 <when value="101_101"></when>
83 </conditional> 104 </conditional>
84 <conditional name="naive_output_cond"> 105 <conditional name="naive_output_cond">
85 <param name="naive_output" type="select" label="Output new IMGT archives per class into your history?"> 106 <param name="naive_output" type="select" label="Output new IMGT archives per class into your history?">
86 <option value="yes">Yes</option> 107 <option value="yes">Yes</option>
87 <option value="no" selected="true">No</option> 108 <option value="no" selected="true">No</option>