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comparison macros.xml @ 0:5b44ef788111 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit aa97817f89e4ac6e7bb2326a51ecbc91830de5df
author iuc
date Wed, 19 Sep 2018 08:21:27 -0400
parents
children 390fc279c3e5
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-1:000000000000 0:5b44ef788111
1 <macros>
2 <xml name="requirements">
3 <requirements>
4 <requirement type="package" version="@TOOL_VERSION@">samtools</requirement>
5 <yield/>
6 </requirements>
7 </xml>
8 <token name="@TOOL_VERSION@">1.9</token>
9 <token name="@FLAGS@">#set $flags = sum(map(int, str($filter).split(',')))</token>
10 <token name="@PREPARE_IDX@"><![CDATA[
11 ##prepare input and indices
12 ln -s '$input' infile &&
13 #if $input.is_of_type('bam'):
14 #if str( $input.metadata.bam_index ) != "None":
15 ln -s '${input.metadata.bam_index}' infile.bai &&
16 #else:
17 samtools index infile infile.bai &&
18 #end if
19 #elif $input.is_of_type('cram'):
20 #if str( $input.metadata.cram_index ) != "None":
21 ln -s '${input.metadata.cram_index}' infile.crai &&
22 #else:
23 samtools index infile infile.crai &&
24 #end if
25 #end if
26 ]]></token>
27 <token name="@PREPARE_IDX_MULTIPLE@"><![CDATA[
28 ##prepare input and indices
29 #for $i, $bam in enumerate( $input_bams ):
30 ln -s '$bam' '${i}' &&
31 #if $bam.is_of_type('bam'):
32 #if str( $bam.metadata.bam_index ) != "None":
33 ln -s '${bam.metadata.bam_index}' '${i}.bai' &&
34 #else:
35 samtools index '${i}' '${i}.bai' &&
36 #end if
37 #elif $bam.is_of_type('cram'):
38 #if str( $bam.metadata.cram_index ) != "None":
39 ln -s '${bam.metadata.cram_index}' '${i}.crai' &&
40 #else:
41 samtools index '${i}' '${i}.crai' &&
42 #end if
43 #end if
44 #end for
45 ]]></token>
46 <token name="@PREPARE_FASTA_IDX@"><![CDATA[
47 ##checks for reference data ($addref_cond.addref_select=="history" or =="cached")
48 ##and sets the -t/-T parameters accordingly:
49 ##- in case of history a symbolic link is used because samtools (view) will generate
50 ## the index which might not be possible in the directory containing the fasta file
51 ##- in case of cached the absolute path is used which allows to read the cram file
52 ## without specifying the reference
53 #if $addref_cond.addref_select == "history":
54 ln -s '${addref_cond.ref}' reference.fa &&
55 samtools faidx reference.fa &&
56 #set reffa=str($addref_cond.ref)
57 #set reffai="reference.fa.fai"
58 #elif $addref_cond.addref_select == "cached":
59 #set reffa=str($addref_cond.ref.fields.path)
60 #set reffai=str($addref_cond.ref.fields.path)
61 #else
62 #set reffa=None
63 #set reffai=None
64 #end if
65 ]]></token>
66 <token name="@ADDTHREADS@"><![CDATA[
67 ##compute the number of ADDITIONAL threads to be used by samtools (-@)
68 addthreads=\${GALAXY_SLOTS:-1} && (( addthreads-- )) &&
69 ]]></token>
70 <xml name="flag_options">
71 <option value="1">read is paired</option>
72 <option value="2">read is mapped in a proper pair</option>
73 <option value="4">read is unmapped</option>
74 <option value="8">mate is unmapped</option>
75 <option value="16">read reverse strand</option>
76 <option value="32">mate reverse strand</option>
77 <option value="64">read is the first in a pair</option>
78 <option value="128">read is the second in a pair</option>
79 <option value="256">alignment or read is not primary</option>
80 <option value="512">read fails platform/vendor quality checks</option>
81 <option value="1024">read is a PCR or optical duplicate</option>
82 <option value="2048">supplementary alignment</option>
83 </xml>
84 <xml name="citations">
85 <citations>
86 <citation type="bibtex">
87 @misc{SAM_def,
88 title={Definition of SAM/BAM format},
89 url = {https://samtools.github.io/hts-specs/},}
90 </citation>
91 <citation type="doi">10.1093/bioinformatics/btp352</citation>
92 <citation type="doi">10.1093/bioinformatics/btr076</citation>
93 <citation type="doi">10.1093/bioinformatics/btr509</citation>
94 <citation type="bibtex">
95 @misc{Danecek_et_al,
96 Author={Danecek, P., Schiffels, S., Durbin, R.},
97 title={Multiallelic calling model in bcftools (-m)},
98 url = {http://samtools.github.io/bcftools/call-m.pdf},}
99 </citation>
100 <citation type="bibtex">
101 @misc{Durbin_VCQC,
102 Author={Durbin, R.},
103 title={Segregation based metric for variant call QC},
104 url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},}
105 </citation>
106 <citation type="bibtex">
107 @misc{Li_SamMath,
108 Author={Li, H.},
109 title={Mathematical Notes on SAMtools Algorithms},
110 url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},}
111 </citation>
112 <citation type="bibtex">
113 @misc{SamTools_github,
114 title={SAMTools GitHub page},
115 url = {https://github.com/samtools/samtools},}
116 </citation>
117 </citations>
118 </xml>
119 <xml name="version_command">
120 <version_command><![CDATA[samtools 2>&1 | grep Version]]></version_command>
121 </xml>
122 <xml name="stdio">
123 <stdio>
124 <exit_code range="1:" level="fatal" description="Error" />
125 </stdio>
126 </xml>
127 </macros>