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comparison macros.xml @ 0:046cbf29795a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
author iuc
date Fri, 28 Sep 2018 04:29:07 -0400
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children a312a0fdaf31
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-1:000000000000 0:046cbf29795a
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="reference.fa"
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)+".fai"
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 <token name="@ADDMEMORY@"><![CDATA[
71 ##compute the number of memory available to samtools sort (-m)
72 ##use only 75% of available: https://github.com/samtools/samtools/issues/831
73 addmemory=\${GALAXY_MEMORY_MB_PER_SLOT:-768} &&
74 ((addmemory=addmemory*75/100)) &&
75 ]]></token>
76 <xml name="seed_input">
77 <param name="seed" type="integer" optional="True" label="Seed for random number generator" help="If empty a random seed is used." />
78 </xml>
79 <xml name="flag_options">
80 <option value="1">read is paired</option>
81 <option value="2">read is mapped in a proper pair</option>
82 <option value="4">read is unmapped</option>
83 <option value="8">mate is unmapped</option>
84 <option value="16">read reverse strand</option>
85 <option value="32">mate reverse strand</option>
86 <option value="64">read is the first in a pair</option>
87 <option value="128">read is the second in a pair</option>
88 <option value="256">alignment or read is not primary</option>
89 <option value="512">read fails platform/vendor quality checks</option>
90 <option value="1024">read is a PCR or optical duplicate</option>
91 <option value="2048">supplementary alignment</option>
92 </xml>
93
94 <!-- region specification macros and tokens for tools that allow the specification
95 of region by bed file / space separated list of regions -->
96 <token name="@REGIONS_FILE@"><![CDATA[
97 #if $cond_region.select_region == 'tab':
98 -t '$cond_region.targetregions'
99 #end if
100 ]]></token>
101 <token name="@REGIONS_MANUAL@"><![CDATA[
102 #if $cond_region.select_region == 'text':
103 #for $i, $x in enumerate($cond_region.regions_repeat):
104 '${x.region}'
105 #end for
106 #end if
107 ]]></token>
108 <xml name="regions_macro">
109 <conditional name="cond_region">
110 <param name="select_region" type="select" label="Filter by regions" help="restricts output to only those alignments which overlap the specified region(s)">
111 <option value="no" selected="True">No</option>
112 <option value="text">Manualy specify regions</option>
113 <option value="tab">Regions from tabular file</option>
114 </param>
115 <when value="no"/>
116 <when value="text">
117 <repeat name="regions_repeat" min="1" default="1" title="Regions">
118 <param name="region" type="text" label="region" help="format chr:from-to">
119 <validator type="regex" message="Required format: CHR[:FROM[-TO]]; where CHR: string containing any character except quotes, whitespace and colon; FROM and TO: any integer">^[^\s'\":]+(:\d+(-\d+){0,1}){0,1}$</validator>
120 </param>
121 </repeat>
122 </when>
123 <when value="tab">
124 <param name="targetregions" argument="-t/--target-regions" type="data" format="tabular" label="Target regions file" help="Do stats in these regions only. Tab-delimited file chr,from,to (1-based, inclusive)" />
125 </when>
126 </conditional>
127 </xml>
128
129 <xml name="citations">
130 <citations>
131 <citation type="bibtex">
132 @misc{SAM_def,
133 title={Definition of SAM/BAM format},
134 url = {https://samtools.github.io/hts-specs/},}
135 </citation>
136 <citation type="doi">10.1093/bioinformatics/btp352</citation>
137 <citation type="doi">10.1093/bioinformatics/btr076</citation>
138 <citation type="doi">10.1093/bioinformatics/btr509</citation>
139 <citation type="bibtex">
140 @misc{Danecek_et_al,
141 Author={Danecek, P., Schiffels, S., Durbin, R.},
142 title={Multiallelic calling model in bcftools (-m)},
143 url = {http://samtools.github.io/bcftools/call-m.pdf},}
144 </citation>
145 <citation type="bibtex">
146 @misc{Durbin_VCQC,
147 Author={Durbin, R.},
148 title={Segregation based metric for variant call QC},
149 url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},}
150 </citation>
151 <citation type="bibtex">
152 @misc{Li_SamMath,
153 Author={Li, H.},
154 title={Mathematical Notes on SAMtools Algorithms},
155 url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},}
156 </citation>
157 <citation type="bibtex">
158 @misc{SamTools_github,
159 title={SAMTools GitHub page},
160 url = {https://github.com/samtools/samtools},}
161 </citation>
162 </citations>
163 </xml>
164 <xml name="version_command">
165 <version_command><![CDATA[samtools 2>&1 | grep Version]]></version_command>
166 </xml>
167 <xml name="stdio">
168 <stdio>
169 <exit_code range="1:" level="fatal" description="Error" />
170 </stdio>
171 </xml>
172 </macros>