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comparison tepid-discover.xml @ 0:a5ef6470e54d draft

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planemo upload for repository https://github.com/ListerLab/TEPID commit c36c280ed14c7afaf6859d37656a7b91ba6944b3-dirty
author mvdbeek
date Thu, 15 Dec 2016 08:33:53 -0500
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children cea423bd0cd2
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-1:000000000000 0:a5ef6470e54d
1 <tool id="tepid_discover" name="tepid-discover" version="@WRAPPER_VERSION@">
2 <description>discover TE variants</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <version_command>tepid-discover --version</version_command>
8 <command detect_errors="exit_code"><![CDATA[
9 @LINK_CONC@
10 tepid-discover
11 $deletions
12 $insertions
13 $strict
14 #if $mask:
15 --mask '$mask'
16 #end if
17 #if $discordant_bam:
18 --discordant '$discordant_bam'
19 #end if
20 @PROC@
21 @NAME@
22 -c conc.bam
23 -s '$split_bam'
24 -t '$te_annotation_bed'
25 $se_mode && ## The follwing is terrible, but from_work_dir cannot deal with variables
26 mv insertions_'$bowtie2_bam.element_identifier'.bed '$insertions_out' &&
27 mv deletions_'$bowtie2_bam.element_identifier'.bed '$deletions_out' &&
28 mv insertion_reads_'$bowtie2_bam.element_identifier'.txt '$insertion_reads_out' &&
29 mv deletion_reads_'$bowtie2_bam.element_identifier'.txt '$deletion_reads_out' &&
30 cat tepid_discover_log_'$bowtie2_bam.element_identifier'.txt
31 ]]></command>
32 <inputs>
33 <param name="bowtie2_bam" label="Alignment file (Bowtie2)" argument="--conc" type="data" format="bam"/>
34 <param name="discordant_bam" label="Alignment file with discordant pairs" argument="--discordant" optional="true" type="data" format="bam"/>
35 <param name="split_bam" label="Alignment file with split reads" argument="--split" type="data" format="bam"/>
36 <param name="mask" type="select" optional="True" label="Select chromosomes that you would like to exclude" multiple="True">
37 <options>
38 <filter type="data_meta" ref="bowtie2_bam" key="reference_names" />
39 </options>
40 </param>
41 <param name="te_annotation_bed" label="BED file with TE locations" argument="--te" type="data" format="bed"/>
42 <param name="se_mode" argument="--se" type="boolean" truevalue="--se" falsevalue="" label="Run in single-end mode?"/>
43 <param name="deletions" argument="--deletions" type="boolean" truevalue="--deletions" falsevalue="" label="Find deletions only?"/>
44 <param name="insertions" argument="--insertions" type="boolean" truevalue="--insertions" falsevalue="" label="Find insertions only?"/>
45 <param name="strict" argument="--strict" type="boolean" truevalue="--strict" falsevalue="" label="Report high-confidence variants only?"/>
46 </inputs>
47 <outputs>
48 <data name="insertions_out" format="bed" label="tepid_discover insertions on ${on_string}"/>
49 <data name="deletions_out" format="bed" label="tepid_discover deletions on ${on_string}"/>
50 <data name="insertion_reads_out" format="txt" label="tepid_discover reads supporting insertions for ${on_string}"/>
51 <data name="deletion_reads_out" format="txt" label="tepid_discover reads supporting deletions for ${on_string}"/>
52 </outputs>
53 <tests>
54 <test>
55 <param name="bowtie2_bam" value="conc.bam"/>
56 <param name="split_bam" value="split.bam"/>
57 <param name="te_annotation_bed" value="TAIR9_TE.bed.gz" ftype="bed"/>
58 <output name="insertions_out" file="insertions_test.bed"/>
59 <output name="deletions_out" file="deletions_test.bed"/>
60 <output name="insertion_reads_out" file="insertion_reads_test.txt"/>
61 <output name="deletion_reads_out" file="deletion_reads_test.txt"/>
62 </test>
63 </tests>
64 <help><![CDATA[
65 TEPID -- transposable element polymorphism identification
66
67 optional arguments:
68 -h, --help show this help message and exit
69 --version show program's version number and exit
70 -k, --keep keep all intermediate files
71 -d, --deletions find deletions only
72 -i, --insertions find insertions only
73 --strict Report high-confidence variants only
74 --mask MASK Mask chromosomes in comma separated list or file
75 -D DISCORDANT, --discordant DISCORDANT
76 Supply discordant reads bam file
77 -p PROC, --proc PROC number of processors
78 -n NAME, --name NAME sample name
79 -c CONC, --conc CONC bam file from bowtie2
80 -s SPLIT, --split SPLIT
81 split reads bam file from yaha
82 -t TE, --te TE TE annotation bedfile
83 --se Run in single-end mode
84 ]]></help>
85 <expand macro="citations"/>
86 </tool>