Mercurial > repos > davidvanzessen > argalaxy_tools

comparison complete_immunerepertoire.xml @ 56:7ae6b6b5d890 draft

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"planemo upload commit 2d4cb6757e8eff095295550bbde6fd9e2ee0b73d"
author rhpvorderman
date Tue, 14 Dec 2021 12:45:47 +0000
parents 2a7dc86d8f85
children 33412e85e669
comparison
equal deleted inserted replaced
55:2a7dc86d8f85 56:7ae6b6b5d890
1 <tool id="complete_immunerepertoire_igg" name="Immune Repertoire pipeline" version="1.0.2"> 1 <tool id="complete_immunerepertoire_igg" name="Immune Repertoire pipeline" version="1.1.0.alpha1">
2 <requirements> 2 <requirements>
3 <requirement type="package" version="2.3">r-gridextra</requirement> 3 <requirement type="package" version="2.3">r-gridextra</requirement>
4 <requirement type="package" version="3.0.0">r-ggplot2</requirement> 4 <requirement type="package" version="3.0.0">r-ggplot2</requirement>
5 <requirement type="package" version="1.8.4">r-plyr</requirement> 5 <requirement type="package" version="1.8.4">r-plyr</requirement>
6 <requirement type="package" version="1.11.4">r-data.table</requirement> 6 <requirement type="package" version="1.11.4">r-data.table</requirement>
8 <requirement type="package" version="1.3.0">r-lymphclon</requirement> 8 <requirement type="package" version="1.3.0">r-lymphclon</requirement>
9 <requirement type="package" version="1.2.4">r-stringi</requirement> 9 <requirement type="package" version="1.2.4">r-stringi</requirement>
10 <requirement type="package" version="1.3.1">r-stringr</requirement> 10 <requirement type="package" version="1.3.1">r-stringr</requirement>
11 <requirement type="package" version="0.69.6">circos</requirement> 11 <requirement type="package" version="0.69.6">circos</requirement>
12 <requirement type="package" version="0.23">circos-tools</requirement> 12 <requirement type="package" version="0.23">circos-tools</requirement>
13 </requirements> 13 <requirement type="package" version="1.34">tar</requirement>
14 <requirement type="package" version="6.0">unzip</requirement>
15 <requirement type="package" version="0.4">unrar</requirement>
16 <requirement type="package" version="16.02">p7zip</requirement>
17 <requirement type="package" version="4.6.0">findutils</requirement>
18 <container type="docker">quay.io/rhpvorderman/mulled-v2-62aaeb9dad7d9973e676594c3aa69e605c73cd0c:80328e762d48b0d7b11c4fa41a5c09ca43d49db9-0</container>
19 </requirements>
14 <description> </description> 20 <description> </description>
15 <command interpreter="bash"> 21 <command interpreter="bash">
16 complete.sh " 22 complete.sh "
17 #for $i, $f in enumerate($patients) 23 #for $i, $f in enumerate($patients)
18 "${f.id}" 24 "${f.id}"
30 <inputs> 36 <inputs>
31 <repeat name="patients" title="Donor" min="1" default="1"> 37 <repeat name="patients" title="Donor" min="1" default="1">
32 <repeat name="samples" title="Replicate" min="1" default="1"> 38 <repeat name="samples" title="Replicate" min="1" default="1">
33 <param name="sample" type="data" label="Replicate to Process" /> 39 <param name="sample" type="data" label="Replicate to Process" />
34 </repeat> 40 </repeat>
35 <param name="id" type="text" label="ID" /> 41 <param name="id" type="text" label="ID">
42 <!-- This replace whitespace with _ -->
43 <sanitizer invalid_char="_" sanitize="true">
44 <valid initial="default"/>
45 </sanitizer>
46 </param>
36 </repeat> 47 </repeat>
37 <param name="clonaltype" type="select" label="Clonal Type Definition"> 48 <param name="clonaltype" type="select" label="Clonal Type Definition">
38 <option value="none">Don't remove duplicates based on clonaltype</option> 49 <option value="none">Don't remove duplicates based on clonaltype</option>
39 <option value="Top.V.Gene,CDR3.Seq">Top.V.Gene, CDR3 (AA)</option> 50 <option value="Top.V.Gene,CDR3.Seq">Top.V.Gene, CDR3 (AA)</option>
40 <option value="Top.V.Gene,CDR3.Seq.DNA">Top.V.Gene, CDR3 (nt)</option> 51 <option value="Top.V.Gene,CDR3.Seq.DNA">Top.V.Gene, CDR3 (nt)</option>