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comparison tepid-refine.xml @ 0:5d1f880c988b draft default tip

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planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
author mvdbeek
date Mon, 23 Jan 2017 10:05:22 -0500
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1 <tool id="tepid-refine" name="tepid-refine" version="0.1.0">
2 <description>refine and genotype TE insertion and deletion calls</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <version_command>tepid-refine --version</version_command>
8 <command detect_errors="exit_code"><![CDATA[
9 @LINK_CONC@
10 ln -s -f '$deletion_readsupport' deletion_reads_'$bowtie2_bam.element_identifier'.txt &&
11 ln -s -f '$insertion_readsupport' insertion_reads_'$bowtie2_bam.element_identifier'.txt &&
12 tepid-refine
13 -i '$insertions'
14 -d '$deletions'
15 -c conc.bam
16 -s '$split_bam'
17 -t '$te_annotation_bed'
18 -a '$all_sample_ids' ## use collection and collapse names in cheetah
19 @PROC@
20 @NAME@ &&
21 mv second_pass_insertion_'$bowtie2_bam.element_identifier'.bed second_pass_insertion.bed &&
22 mv ambiguous_insertion_'$bowtie2_bam.element_identifier'.bed ambiguous_insertion.bed &&
23 mv second_pass_reads_insertion_'$bowtie2_bam.element_identifier'.txt second_pass_reads_insertion.txt &&
24 mv second_pass_deletion_'$bowtie2_bam.element_identifier'.bed second_pass_deletion.bed &&
25 mv ambiguous_deletion_'$bowtie2_bam.element_identifier'.bed ambiguous_deletion.bed &&
26 mv second_pass_reads_deletion_'$bowtie2_bam.element_identifier'.txt second_pass_reads_deletion.txt
27 ]]></command>
28 <configfiles>
29 <configfile name="all_sample_ids">#if $sample_id_source.source == 'enter':
30 #set $sample_list = "\n".join([x for x in str($sample_id_source.sample_ids).split(',')])
31 #else
32 #set $sample_list = "\n".join([str(x.element_identifier) for x in $sample_id_source.sample_ids])
33 #end if
34 $sample_list</configfile>
35 </configfiles>
36 <inputs>
37 <param name="bowtie2_bam" argument="--conc" type="data" format="bam"/>
38 <param name="split_bam" argument="--split" type="data" format="bam"/>
39 <param name="insertion_readsupport" type="data" format="txt"/>
40 <param name="deletion_readsupport" type="data" format="txt"/>
41 <param name="insertions" argument="--insertions" type="data" format="bed" help="Merged insertions"/>
42 <param name="deletions" argument="--deletions" type="data" format="bed" help="Merged and flipped deletions"/>
43 <param name="te_annotation_bed" argument="--te" type="data" format="bed"/>
44 <conditional name="sample_id_source">
45 <param name="source" type="select">
46 <option value="enter">Enter all sample ids</option>
47 <option value="auto">Infer sample IDs from collection identifiers</option>
48 </param>
49 <when value="enter">
50 <param name="sample_ids" type="text"/>
51 </when>
52 <when value="auto">
53 <param name="sample_ids" type="data_collection" collection_type="list"/>
54 </when>
55 </conditional>
56 </inputs>
57 <outputs>
58 <data name="refined_insertions" format="bed" from_work_dir="second_pass_insertion.bed" label="Refined insertions"/>
59 <data name="ambiguous_insertions" format="bed" from_work_dir="ambiguous_insertion.bed" label="Amibguous insertions"/>
60 <data name="second_pass_insertion_support" format="txt" from_work_dir="second_pass_reads_insertion.txt" label="Second pass insertion readsupport"/>
61 <data name="refined_deletions" format="bed" from_work_dir="second_pass_deletion.bed" label="Refined deletions"/>
62 <data name="ambiguous_deletions" format="bed" from_work_dir="ambiguous_deletion.bed" label="Ambiguous deletions"/>
63 <data name="second_pass_deletion_support" format="txt" from_work_dir="second_pass_reads_deletion.txt" label="Second pass deletion readsupport"/>
64 </outputs>
65 <tests>
66 <test>
67 <param name="bowtie2_bam" value="conc.bam"/>
68 <param name="split_bam" value="split.bam"/>
69 <param name="insertion_readsupport" value="insertion_reads_2.txt"/>
70 <param name="deletion_readsupport" value="deletion_reads_2.txt"/>
71 <param name="insertions" value="merged_insertions.bed" ftype="bed"/>
72 <param name="deletions" value="merged_flipped_deletions.bed" ftype="bed"/>
73 <param name="te_annotation_bed" value="te.bed" ftype="bed"/>
74 <param name="source" value="enter"/>
75 <param name="sample_ids" value="1,conc.bam"/>
76 <output name="refined_insertions" file="second_pass_insertion_2.bed"/>
77 <output name="refined_deletions" file="second_pass_deletion_2.bed"/>
78 </test>
79 </tests>
80 <help><![CDATA[
81 TEPID -- refine TE insertion and deletion calls
82
83 optional arguments:
84 -h, --help show this help message and exit
85 --version show program's version number and exit
86 -k, --keep keep all intermediate files
87 -i INSERTIONS, --insertions INSERTIONS
88 File containing collapsed TE insertions for all
89 samples in population
90 -d DELETIONS, --deletions DELETIONS
91 File containing collapsed TE deletions for all samples
92 in population
93 -p PROC, --proc PROC number of processors
94 -t TE, --te TE TE annotation bedfile
95 -n NAME, --name NAME sample name
96 -c CONC, --conc CONC bam file from bowtie2
97 -s SPLIT, --split SPLIT
98 split reads bam file from yaha
99 -a ALL_SAMPLES, --all_samples ALL_SAMPLES
100 List of all sample names
101 ]]></help>
102 <expand macro="citations"/>
103 </tool>