Mercurial > repos > yhoogstrate > varscan_mpileup2indel_from_bam

annotate varscan_mpileup2indel_from_bam.xml @ 0:10e2ea79ec55 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
author yhoogstrate
date Thu, 05 Nov 2015 10:00:19 -0500
parents
children 2c56a59a112f
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
1 <?xml version="1.0" encoding="UTF-8"?>
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
2 <tool id="varscan_mpileup2indel_from_bam" name="VarScan2 Call INDELs from BAM" version="2.3.6.a">
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
3 <description>VarScan2 INDEL detection; directly reading *.bam file(s) &amp; using parallel mpileup generation, to avoid unnecessairy I/O overhead and increase performance.</description>
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
4
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
5 <requirements>
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
6 <requirement type="package" version="0.1.19a">samtools_parallel_mpileup_0_1_19a</requirement>
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
7 <requirement type="package" version="0.1.19">samtools</requirement>
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
8 <requirement type="package" version="2.3.6">varscan</requirement>
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
9 </requirements>
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
10
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
11 <version_command>java -jar $JAVA_JAR_PATH/VarScan.v2.3.6.jar 2>&amp;1 | head -n 1</version_command>
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
12
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
13 <command>
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
14 #if $reference_genome_source.source_select == "attribute" and len({ alignment.metadata.dbkey:True for alignment in $alignments }.keys()) != 1
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
15 echo "Invalid number of dbkeys are found: ${ len({ alignment.metadata.dbkey:True for alignment in $alignments }.keys()) }, while only one should be used. Make sure that the alignments are done on the same reference genome and that 'tool-data/all_fasta.loc' is configured properly!" >&amp;2
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
16 #else
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
17 #import os.path
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
18 #for $alignment in $alignments
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
19 <!-- @todo use the existence of $alignment.metadata.bam_index or $alignment.metadata['bam_index'] -->
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
20 #if not os.path.isfile(str($alignment)+".bai")
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
21 echo "- Indexing alignment file: $alignment.name " ;
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
22 samtools index $alignment 2>&amp;1 ;
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
23 #else
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
24 echo "- Skiping indexing: $alignment.name " ;
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
25 #end if
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
26 #end for
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
27
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
28 #if $mpileup_parallelization.mpileup_parallelization_select == "true"
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
29 samtools-parallel-mpileup mpileup
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
30 -t $mpileup_parallelization.samtools_threads
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
31 #else
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
32 samtools mpileup
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
33 #end if
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
34 -f
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
35 #if $reference_genome_source.source_select == "indexed_filtered"
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
36 "$reference_genome_source.reference_genome"
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
37 #else if $reference_genome_source.source_select == "indexed_all"
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
38 "$reference_genome_source.reference_genome"
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
39 #else if $reference_genome_source.source_select == "history"
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
40 "$reference_genome_source.reference_genome"
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
41 #else
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
42 <!--
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
43 This is a workaround to obtain the "genome.fa" file that
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
44 corresponds to the dbkey of the alignments.
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
45 Because this file is "calculated" during run-time, it can
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
46 be used in a workflow.
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
47 -->
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
48 "${ filter( lambda x: str( x[0] ) == str( { alignment.metadata.dbkey:True for alignment in $alignments }.keys()[0] ), $__app__.tool_data_tables[ 'all_fasta' ].get_fields() )[0][-1] }"
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
49 #end if
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
50
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
51 #if $extended_parameters_regions.samtools_regions == "region"
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
52 -r $extended_parameters_regions.samtools_r
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
53 #elif $extended_parameters_regions.samtools_regions == "regions_file_pos" or $extended_parameters_regions.samtools_regions == "regions_file_bed"
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
54 -l $extended_parameters_regions.samtools_l
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
55 #end if
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
56
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
57 #if $extended_parameters.parameters == "extended"
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
58 $extended_parameters.samtools_6
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
59 $extended_parameters.samtools_A
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
60 $extended_parameters.samtools_B
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
61 -C $extended_parameters.samtools_C
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
62 -d $extended_parameters.samtools_d
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
63 $extended_parameters.samtools_E
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
64 -M $extended_parameters.samtools_M
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
65 $extended_parameters.samtools_R
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
66 -q $extended_parameters.samtools_q
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
67 -Q $extended_parameters.samtools_Q
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
68
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
69 -e $extended_parameters.samtools_e
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
70 -F $extended_parameters.samtools_F
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
71 -h $extended_parameters.samtools_h
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
72 $extended_parameters.samtools_I
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
73 -L $extended_parameters.samtools_L
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
74 -m $extended_parameters.samtools_m
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
75 -o $extended_parameters.samtools_o
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
76 $extended_parameters.samtools_p
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
77 -P $extended_parameters.samtools_P
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
78 #end if
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
79
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
80 #for $alignment in $alignments
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
81 ${alignment}
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
82 #end for
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
83 2>stderr_1.txt
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
84
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
85 #if $mpileup_parallelization.mpileup_parallelization_select == "true"
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
86 #if $mpileup_parallelization.sort_mpileup
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
87 | sort -k1,1V -k2,2g
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
88 #end if
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
89 #end if
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
90
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
91 | java
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
92 -Xmx64G
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
93 -jar \$JAVA_JAR_PATH/VarScan.v2.3.6.jar
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
94 mpileup2indel
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
95
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
96 #if $extended_parameters.parameters == "extended"
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
97 --min-coverage $extended_parameters.varscan_min_coverage
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
98 --min-reads2 $extended_parameters.varscan_min_reads2
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
99 --min-avg-qual $extended_parameters.varscan_min_avg_qual
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
100 --min-var-freq $extended_parameters.varscan_min_var_freq
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
101 --min-freq-for-hom $extended_parameters.varscan_min_freq_for_hom
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
102 --p-value $extended_parameters.varscan_p_value
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
103 $extended_parameters.varscan_strand_filter
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
104 $extended_parameters.varscan_variants
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
105 #end if
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
106
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
107 #if $varscan_output == "vcf" or $varscan_output.value == "vcf"
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
108 --output-vcf 1
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
109 #end if
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
110
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
111 2>stderr_2.txt
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
112 > $snv_output ;
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
113
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
114
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
115 echo "---------------[ mpileup generation ]---------------" ;
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
116 cat stderr_1.txt ;
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
117 echo "" ;
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
118 echo "---------------[ VarScan INDEL detect ]-------------" ;
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
119 cat stderr_2.txt ;
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
120 echo "" ;
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
121 echo "----------------------------------------------------" ;
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
122 #end if
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
123 </command>
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
124
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
125 <inputs>
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
126 <param format="bam,sam" multiple="true" name="alignments" type="data" label="Alignment file(s)" help="Mapped reads in BAM or SAM format."/>
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
127
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
128 <!-- Find out how to access the reference genome from the BAM file(s) -->
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
129 <conditional name="reference_genome_source">
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
130 <param name="source_select" type="select" label="Fasta Source">
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
131 <option value="indexed_filtered">Use a built-in index (which fits your reference)</option>
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
132 <option value="history">Use reference from the history</option>
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
133 <option value="indexed_all">Use a built-in index (entire list) - avoid this option if possible; only useful if you design a workflow</option>
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
134 <option value="attribute">Use a built-in index based on the 'metadata.dbkey' attribute; ideal in workflows</option>
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
135 </param>
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
136 <when value="history">
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
137 <param name="reference_genome" format="fasta" type="data" label="Reference Genome used during alignment (FASTA)" help="Reference genome (genome.fa) that corresponds to the *.bam file." />
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
138 </when>
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
139 <when value="indexed_filtered">
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
140 <param name="reference_genome" type="select" label="Reference Genome used during alignment (FASTA)" >
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
141 <options from_data_table="all_fasta">
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
142 <column name="name" index="2"/>
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
143 <column name="dbkey" index="1"/>
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
144 <column name="value" index="3"/><!-- Value is the path of the fasta file -->
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
145 <filter type="data_meta" ref="alignments" multiple="false" key="dbkey" column="1" />
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
146 <validator type="no_options" message="No indexes are available for the selected input dataset" />
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
147 </options>
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
148 </param>
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
149 </when>
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
150 <when value="indexed_all">
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
151 <param name="reference_genome" type="select" label="Reference Genome used during alignment (FASTA)" >
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
152 <options from_data_table="all_fasta">
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
153 <column name="name" index="2"/>
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
154 <column name="dbkey" index="1"/>
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
155 <column name="value" index="3"/><!-- Value is the path of the fasta file -->
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
156 <validator type="no_options" message="No indexes are available for the selected input dataset" />
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
157 </options>
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
158 </param>
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
159 </when>
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
160 <when value="attribute" />
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
161 </conditional>
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
162
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
163 <conditional name="extended_parameters_regions">
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
164 <param name="samtools_regions" type="select" label="Region specific parameters" help="Let samtools target specific genomic locations.">
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
165 <option value="entire_genome">Entire genome</option>
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
166 <option value="region">Specific region</option>
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
167 <option value="regions_file_pos">Specific positions (file); list of positions</option>
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
168 <option value="regions_file_bed">Specific regions (file); list of regions in BED</option>
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
169 </param>
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
170 <when value="entire_genome" />
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
171 <when value="region">
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
172 <param type="text" name="samtools_r" label="Samtools: region in which pileup is generated" help="e.g. chrX or chr:pos or chr:start-end" />
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
173 </when>
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
174 <when value="regions_file_pos">
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
175 <param type="data" name="samtools_l" format="tabular" label="Samtools: list of positions (chr pos)" />
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
176 </when>
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
177 <when value="regions_file_bed">
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
178 <param type="data" name="samtools_l" format="bed" label="Samtools: specific regions (BED)" />
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
179 </when>
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
180 </conditional>
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
181
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
182 <conditional name="mpileup_parallelization">
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
183 <param name="mpileup_parallelization_select" type="select" label="Use parallelization for the mpileup generation (experimental)" help="Especially if larger numbers of bam/sam files are processed, or the file infrastructure is optimized for IO-paralellization, this feature might improve performance.">
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
184 <option value="false" >False - uses classical samtools</option>
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
185 <option value="true">True - uses (experimental) samtools mpileup-parallel</option>
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
186 </param>
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
187 <when value="false" />
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
188 <when value="true">
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
189 <param type="integer" name="samtools_threads" value="2" min="1" label="Samtools: mpileup threads" />
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
190 <param type="boolean" name="sort_mpileup" truevalue="true" falsevalue="false" label="Sort mpileup file (SLOW)" help="Because parallelization may disrupt the outputs order, sorting can be conveniet for e.g. testing. Notice that this function has only use in a limited number of situations but consumes (much) resources. Only use it if it's really neccesairy." />
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
191 </when>
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
192 </conditional>
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
193
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
194 <conditional name="extended_parameters">
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
195 <param name="parameters" type="select" label="Advanced parameters" help="For more advanced VarScan and samtools settings.">
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
196 <option value="default">Default settings</option>
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
197 <option value="extended">Extended settings</option>
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
198 </param>
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
199 <when value="default" />
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
200 <when value="extended">
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
201 <param type="boolean" name="samtools_6" falsevalue="" truevalue=" -6" label="Samtools: assume the quality is in the Illumina-1.3+ encoding" />
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
202 <param type="boolean" name="samtools_A" falsevalue="" truevalue=" -A" label="Samtools: count anomalous read pairs" />
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
203 <param type="boolean" name="samtools_B" falsevalue="" truevalue=" -B" label="Samtools: disable BAQ computation" />
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
204 <param type="integer" name="samtools_C" value="0" label="Samtools: parameter for adjusting mapQ; 0 to disable [0]" />
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
205 <param type="integer" name="samtools_d" value="250" label="Samtools: max per-BAM depth to avoid excessive memory usage [250]" />
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
206 <param type="boolean" name="samtools_E" falsevalue="" truevalue=" -E" label="Samtools: recalculate extended BAQ on the fly thus ignoring existing BQs" />
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
207 <param type="integer" name="samtools_M" value="60" label="cap mapping quality at INT [60]" />
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
208 <param type="boolean" name="samtools_R" falsevalue="" truevalue=" -R" label="Samtools: ignore RG tags" />
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
209 <param type="integer" name="samtools_q" value="0" label="Samtools: skip alignments with mapQ smaller than INT [0]" />
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
210 <param type="integer" name="samtools_Q" value="13" label="Samtools: skip bases with baseQ/BAQ smaller than INT [13]" />
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
211
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
212 <param type="integer" name="samtools_e" value="20" label="Samtools: Phred-scaled gap extension seq error probability [20]" />
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
213 <param type="float" name="samtools_F" value="0.002" label="Samtools: minimum fraction of gapped reads for candidates [0.002]" help="Alias: -F" />
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
214 <param type="integer" name="samtools_h" value="100" label="Samtools: coefficient for homopolymer errors [100]" />
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
215 <param type="boolean" name="samtools_I" falsevalue="" truevalue=" -I" label="Samtools: do not perform indel calling" />
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
216 <param type="integer" name="samtools_L" value="250" label="Samtools: max per-sample depth for INDEL calling [250]" />
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
217 <param type="integer" name="samtools_m" value="1" label="Samtools: minimum gapped reads for indel candidates [1]" help="Alias: -m" />
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
218 <param type="integer" name="samtools_o" value="40" label="Samtools: Phred-scaled gap open sequencing error probability [40]" />
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
219 <param type="boolean" name="samtools_p" falsevalue="" truevalue=" -p" label="Samtools: apply -m and -F per-sample to increase sensitivity" />
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
220 <param type="text" name="samtools_P" value="all" label="Samtools: comma separated list of platforms for indels [all]" />
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
221
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
222 <param type="integer" name="varscan_min_coverage" value="8" label="VarScan: Minimum read depth at a position to make a call [8]" />
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
223 <param type="integer" name="varscan_min_reads2" value="2" label="VarScan: PMinimum supporting reads at a position to call variants [2]" />
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
224 <param type="integer" name="varscan_min_avg_qual" value="15" label="VarScan: Minimum base quality at a position to count a read [15]" />
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
225 <param type="float" name="varscan_min_var_freq" value="0.01" label="VarScan: minimum fraction of gapped reads for candidates [0.002]" help="Alias: -F" />
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
226 <param type="float" name="varscan_min_freq_for_hom" value="0.75" label="VarScan: Minimum frequency to call homozygote [0.75]" />
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
227 <param type="float" name="varscan_p_value" value="0.99" label="VarScan: Default p-value threshold for calling variants [99e-02]" />
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
228 <param type="boolean" name="varscan_strand_filter" falsevalue=" --strand_filter 0" truevalue=" --strand_filter 1" checked="true" label="VarScan: Ignore variants with >90% support on one strand [1]" />
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
229 <param type="boolean" name="varscan_variants" falsevalue=" --variants 0" truevalue=" --variants 1" checked="false" label="VarScan: Report only variant (SNP/indel) positions [0]" />
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
230 </when>
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
231 </conditional>
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
232
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
233 <param name="varscan_output" type="select" label="Output format">
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
234 <option value="vcf">VCF</option>
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
235 <option value="tabular">tabular</option>
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
236 </param>
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
237 </inputs>
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
238
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
239 <outputs>
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
240 <data format="tabular" name="snv_output" label="${tool.name} on ${', '.join([ str(a.hid)+': '+a.name for a in $alignments ])}">
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
241 <change_format>
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
242 <when input="varscan_output" value="vcf" format="vcf" />
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
243 </change_format>
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
244 </data>
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
245 </outputs>
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
246
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
247 <tests>
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
248 <test><!-- Use classical samtools -->
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
249 <param name="alignments" value="example.bam" ftype="bam" />
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
250
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
251 <param name="source_select" value="history" />
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
252 <param name="reference_genome" value="example.fa" ftype="fasta" />
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
253
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
254 <param name="samtools_regions" value="entire_genome" />
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
255
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
256 <param name="mpileup_parallelization_select" value="false" />
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
257 <param name="sort_mpileup" value="true" />
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
258
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
259 <param name="parameters" value="default" />
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
260 <param name="varscan_output_vcf" value="1" />
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
261
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
262
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
263 <output name="snv_output" file="example.vcf" />
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
264 </test>
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
265 <test><!-- Use parallelized samtools -->
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
266 <param name="alignments" value="example.bam" ftype="bam" />
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
267
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
268 <param name="source_select" value="history" />
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
269 <param name="reference_genome" value="example.fa" ftype="fasta" />
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
270
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
271 <param name="samtools_regions" value="entire_genome" />
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
272
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
273 <param name="mpileup_parallelization_select" value="true" />
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
274 <param name="samtools_threads" value="2" />
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
275 <param name="sort_mpileup" value="true" />
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
276
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
277 <param name="parameters" value="default" />
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
278 <param name="varscan_output_vcf" value="1" />
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
279
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
280
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
281 <output name="snv_output" file="example.vcf" />
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
282 </test>
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
283 </tests>
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
284
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
285 <help>
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
286 **VarScan 2.3.6**
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
287
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
288 VarScan is a platform-independent mutation caller for targeted, exome, and whole-genome resequencing data generated on Illumina, SOLiD, Life/PGM, Roche/454, and similar instruments. The newest version, VarScan 2, is written in Java, so it runs on most operating systems.
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
289 http://dx.doi.org/10.1101/gr.129684.111
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
290 http://www.ncbi.nlm.nih.gov/pubmed/19542151
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
291
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
292 *VarScan* requires mpileup formatted input files, which are generally derived from BAM files. Since mpileup files can become humongous, the interim step of storing it is bypassed. Thus, in this wrapper one or multiple BAM/SAM files go in, get processed into a mpileup file and get directly linked to VarScan.
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
293 The samtools package is not able to parallelize the mpileup generation which make it a very slow process.
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
294 Other people were aware of this and have written a version that can do parallelization:
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
295 https://github.com/mydatascience/parallel-mpileup
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
296
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
297 Consequently, when a BAM files gets processed by this wrapper, it's processed by *parallel-mpileup* before its send to VarScan.
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
298
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
299 .. _VarScan: http://varscan.sourceforge.net/
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
300
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
301 **Input formats**
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
302
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
303 VarScan2 accepts sequencing alignments in the same, either SAM or BAM format (http://samtools.sourceforge.net/). The alignment files have to be linked to a reference genome by galaxy. This is indicated under every history item with e.g.: *"database: hg19"* for a link to hg19, or *"database: ?"* if the link is missing.
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
304
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
305 **Installation**
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
306
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
307 Make sure your reference genomes are properly annotated in "tool-data/all_fasta.loc", and linked to the names of the reference used for alignment.
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
308
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
309 **License**
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
310
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
311 * VarScan2.3.6: Non-Profit Open Software License 3.0 (Non-Profit OSL 3.0)
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
312 * parallel-mpileup: MIT License (https://github.com/mydatascience/parallel-mpileup/blob/master/samtools-0.1.19/COPYING)
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
313
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
314
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
315 Contact
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
316 -------
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
317
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
318 The tool wrapper has been written by Youri Hoogstrate from the Erasmus
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
319 Medical Center (Rotterdam, Netherlands) on behalf of the Translational
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
320 Research IT (TraIT) project:
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
321
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
322 http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
323
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
324 More tools by the Translational Research IT (TraIT) project can be found
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
325 in the following toolsheds:
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
326
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
327 http://toolshed.g2.bx.psu.edu/
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
328
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
329 http://testtoolshed.g2.bx.psu.edu/
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
330 </help>
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
331 <citations>
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
332 <citation type="doi">10.1101/gr.129684.111</citation>
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
333 </citations>
10e2ea79ec55 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit 0bc9864516071632199ddf9a4ff403893060c99f
yhoogstrate
parents:
diff changeset
334 </tool>