Mercurial > repos > mvdbeek > tepid_refine

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
author mvdbeek
date Mon, 23 Jan 2017 10:05:22 -0500
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
1 <tool id="tepid-refine" name="tepid-refine" version="0.1.0">
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
2 <description>refine and genotype TE insertion and deletion calls</description>
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
3 <macros>
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
4 <import>macros.xml</import>
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
5 </macros>
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
6 <expand macro="requirements"/>
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
7 <version_command>tepid-refine --version</version_command>
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
8 <command detect_errors="exit_code"><![CDATA[
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
9 @LINK_CONC@
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
10 ln -s -f '$deletion_readsupport' deletion_reads_'$bowtie2_bam.element_identifier'.txt &&
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
11 ln -s -f '$insertion_readsupport' insertion_reads_'$bowtie2_bam.element_identifier'.txt &&
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
12 tepid-refine
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
13 -i '$insertions'
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
14 -d '$deletions'
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
15 -c conc.bam
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
16 -s '$split_bam'
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
17 -t '$te_annotation_bed'
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
18 -a '$all_sample_ids' ## use collection and collapse names in cheetah
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
19 @PROC@
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
20 @NAME@ &&
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
21 mv second_pass_insertion_'$bowtie2_bam.element_identifier'.bed second_pass_insertion.bed &&
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
22 mv ambiguous_insertion_'$bowtie2_bam.element_identifier'.bed ambiguous_insertion.bed &&
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
23 mv second_pass_reads_insertion_'$bowtie2_bam.element_identifier'.txt second_pass_reads_insertion.txt &&
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
24 mv second_pass_deletion_'$bowtie2_bam.element_identifier'.bed second_pass_deletion.bed &&
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
25 mv ambiguous_deletion_'$bowtie2_bam.element_identifier'.bed ambiguous_deletion.bed &&
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
26 mv second_pass_reads_deletion_'$bowtie2_bam.element_identifier'.txt second_pass_reads_deletion.txt
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
27 ]]></command>
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
28 <configfiles>
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
29 <configfile name="all_sample_ids">#if $sample_id_source.source == 'enter':
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
30 #set $sample_list = "\n".join([x for x in str($sample_id_source.sample_ids).split(',')])
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
31 #else
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
32 #set $sample_list = "\n".join([str(x.element_identifier) for x in $sample_id_source.sample_ids])
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
33 #end if
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
34 $sample_list</configfile>
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
35 </configfiles>
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
36 <inputs>
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
37 <param name="bowtie2_bam" argument="--conc" type="data" format="bam"/>
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
38 <param name="split_bam" argument="--split" type="data" format="bam"/>
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
39 <param name="insertion_readsupport" type="data" format="txt"/>
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
40 <param name="deletion_readsupport" type="data" format="txt"/>
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
41 <param name="insertions" argument="--insertions" type="data" format="bed" help="Merged insertions"/>
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
42 <param name="deletions" argument="--deletions" type="data" format="bed" help="Merged and flipped deletions"/>
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
43 <param name="te_annotation_bed" argument="--te" type="data" format="bed"/>
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
44 <conditional name="sample_id_source">
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
45 <param name="source" type="select">
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
46 <option value="enter">Enter all sample ids</option>
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
47 <option value="auto">Infer sample IDs from collection identifiers</option>
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
48 </param>
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
49 <when value="enter">
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
50 <param name="sample_ids" type="text"/>
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
51 </when>
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
52 <when value="auto">
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
53 <param name="sample_ids" type="data_collection" collection_type="list"/>
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
54 </when>
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
55 </conditional>
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
56 </inputs>
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
57 <outputs>
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
58 <data name="refined_insertions" format="bed" from_work_dir="second_pass_insertion.bed" label="Refined insertions"/>
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
59 <data name="ambiguous_insertions" format="bed" from_work_dir="ambiguous_insertion.bed" label="Amibguous insertions"/>
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
60 <data name="second_pass_insertion_support" format="txt" from_work_dir="second_pass_reads_insertion.txt" label="Second pass insertion readsupport"/>
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
61 <data name="refined_deletions" format="bed" from_work_dir="second_pass_deletion.bed" label="Refined deletions"/>
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
62 <data name="ambiguous_deletions" format="bed" from_work_dir="ambiguous_deletion.bed" label="Ambiguous deletions"/>
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
63 <data name="second_pass_deletion_support" format="txt" from_work_dir="second_pass_reads_deletion.txt" label="Second pass deletion readsupport"/>
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
64 </outputs>
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
65 <tests>
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
66 <test>
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
67 <param name="bowtie2_bam" value="conc.bam"/>
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
68 <param name="split_bam" value="split.bam"/>
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
69 <param name="insertion_readsupport" value="insertion_reads_2.txt"/>
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
70 <param name="deletion_readsupport" value="deletion_reads_2.txt"/>
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
71 <param name="insertions" value="merged_insertions.bed" ftype="bed"/>
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
72 <param name="deletions" value="merged_flipped_deletions.bed" ftype="bed"/>
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
73 <param name="te_annotation_bed" value="te.bed" ftype="bed"/>
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
74 <param name="source" value="enter"/>
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
75 <param name="sample_ids" value="1,conc.bam"/>
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
76 <output name="refined_insertions" file="second_pass_insertion_2.bed"/>
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
77 <output name="refined_deletions" file="second_pass_deletion_2.bed"/>
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
78 </test>
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
79 </tests>
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
80 <help><![CDATA[
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
81 TEPID -- refine TE insertion and deletion calls
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
82
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
83 optional arguments:
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
84 -h, --help show this help message and exit
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
85 --version show program's version number and exit
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
86 -k, --keep keep all intermediate files
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
87 -i INSERTIONS, --insertions INSERTIONS
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
88 File containing collapsed TE insertions for all
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
89 samples in population
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
90 -d DELETIONS, --deletions DELETIONS
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
91 File containing collapsed TE deletions for all samples
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
92 in population
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
93 -p PROC, --proc PROC number of processors
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
94 -t TE, --te TE TE annotation bedfile
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
95 -n NAME, --name NAME sample name
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
96 -c CONC, --conc CONC bam file from bowtie2
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
97 -s SPLIT, --split SPLIT
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
98 split reads bam file from yaha
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
99 -a ALL_SAMPLES, --all_samples ALL_SAMPLES
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
100 List of all sample names
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
101 ]]></help>
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
102 <expand macro="citations"/>
5d1f880c988b planemo upload for repository https://github.com/ListerLab/TEPID commit 82fd0448ff5baa9822a388aee78753e4b1cd94d7
mvdbeek
parents:
diff changeset
103 </tool>