|
0
|
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@">1.13</token>
|
|
|
9 <token name="@PROFILE@">20.05</token>
|
|
|
10 <token name="@FLAGS@"><![CDATA[
|
|
|
11 #set $flags = 0
|
|
|
12 #if $filter
|
|
|
13 #set $flags = sum(map(int, str($filter).split(',')))
|
|
|
14 #end if
|
|
|
15 ]]></token>
|
|
|
16 <token name="@PREPARE_IDX@"><![CDATA[
|
|
|
17 ##prepare input and indices
|
|
|
18 ln -s '$input' infile &&
|
|
|
19 #if $input.is_of_type('bam'):
|
|
|
20 #if str( $input.metadata.bam_index ) != "None":
|
|
|
21 ln -s '${input.metadata.bam_index}' infile.bai &&
|
|
|
22 #else:
|
|
|
23 samtools index infile infile.bai &&
|
|
|
24 #end if
|
|
|
25 #elif $input.is_of_type('cram'):
|
|
|
26 #if str( $input.metadata.cram_index ) != "None":
|
|
|
27 ln -s '${input.metadata.cram_index}' infile.crai &&
|
|
|
28 #else:
|
|
|
29 samtools index infile infile.crai &&
|
|
|
30 #end if
|
|
|
31 #end if
|
|
|
32 ]]></token>
|
|
|
33 <token name="@PREPARE_IDX_MULTIPLE@"><![CDATA[
|
|
|
34 ##prepare input and indices
|
|
|
35 #for $i, $bam in enumerate( $input_bams ):
|
|
|
36 ln -s '$bam' '${i}' &&
|
|
|
37 #if $bam.is_of_type('bam'):
|
|
|
38 #if str( $bam.metadata.bam_index ) != "None":
|
|
|
39 ln -s '${bam.metadata.bam_index}' '${i}.bai' &&
|
|
|
40 #else:
|
|
|
41 samtools index '${i}' '${i}.bai' &&
|
|
|
42 #end if
|
|
|
43 #elif $bam.is_of_type('cram'):
|
|
|
44 #if str( $bam.metadata.cram_index ) != "None":
|
|
|
45 ln -s '${bam.metadata.cram_index}' '${i}.crai' &&
|
|
|
46 #else:
|
|
|
47 samtools index '${i}' '${i}.crai' &&
|
|
|
48 #end if
|
|
|
49 #end if
|
|
|
50 #end for
|
|
|
51 ]]></token>
|
|
|
52 <token name="@PREPARE_FASTA_IDX@"><![CDATA[
|
|
|
53 ##checks for reference data ($addref_cond.addref_select=="history" or =="cached")
|
|
|
54 ##and sets the -t/-T parameters accordingly:
|
|
|
55 ##- in case of history a symbolic link is used because samtools (view) will generate
|
|
|
56 ## the index which might not be possible in the directory containing the fasta file
|
|
|
57 ##- in case of cached the absolute path is used which allows to read the cram file
|
|
|
58 ## without specifying the reference
|
|
|
59 #if $addref_cond.addref_select == "history":
|
|
|
60 ln -s '${addref_cond.ref}' reference.fa &&
|
|
|
61 samtools faidx reference.fa &&
|
|
|
62 #set reffa="reference.fa"
|
|
|
63 #set reffai="reference.fa.fai"
|
|
|
64 #elif $addref_cond.addref_select == "cached":
|
|
|
65 #set reffa=str($addref_cond.ref.fields.path)
|
|
|
66 #set reffai=str($addref_cond.ref.fields.path)+".fai"
|
|
|
67 #else
|
|
|
68 #set reffa=None
|
|
|
69 #set reffai=None
|
|
|
70 #end if
|
|
|
71 ]]></token>
|
|
|
72
|
|
|
73 <xml name="optional_reference">
|
|
|
74 <conditional name="addref_cond">
|
|
|
75 <param name="addref_select" type="select" label="Use a reference sequence">
|
|
|
76 <help>@HELP@</help>
|
|
|
77 <option value="no">No</option>
|
|
|
78 <option value="history">Use a genome/index from the history</option>
|
|
|
79 <option value="cached">Use a built-in genome</option>
|
|
|
80 </param>
|
|
|
81 <when value="no"/>
|
|
|
82 <when value="history">
|
|
|
83 <param name="ref" argument="@ARGUMENT@" type="data" format="fasta,fasta.gz" label="Reference"/>
|
|
|
84 </when>
|
|
|
85 <when value="cached">
|
|
|
86 <param name="ref" argument="@ARGUMENT@" type="select" label="Reference">
|
|
|
87 <options from_data_table="fasta_indexes">
|
|
|
88 <filter type="data_meta" ref="input" key="dbkey" column="dbkey"/>
|
|
|
89 </options>
|
|
|
90 <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset"/>
|
|
|
91 </param>
|
|
|
92 </when>
|
|
|
93 </conditional>
|
|
|
94 </xml>
|
|
|
95 <xml name="mandatory_reference" token_help="" token_argument="">
|
|
|
96 <conditional name="addref_cond">
|
|
|
97 <param name="addref_select" type="select" label="Use a reference sequence">
|
|
|
98 <help>@HELP@</help>
|
|
|
99 <option value="history">Use a genome/index from the history</option>
|
|
|
100 <option value="cached">Use a built-in genome</option>
|
|
|
101 </param>
|
|
|
102 <when value="history">
|
|
|
103 <param name="ref" argument="@ARGUMENT@" type="data" format="fasta,fasta.gz" label="Reference"/>
|
|
|
104 </when>
|
|
|
105 <when value="cached">
|
|
|
106 <param name="ref" argument="@ARGUMENT@" type="select" label="Reference">
|
|
|
107 <options from_data_table="fasta_indexes">
|
|
|
108 <filter type="data_meta" ref="input" key="dbkey" column="dbkey"/>
|
|
|
109 <validator message="No reference genome is available for the build associated with the selected input dataset" type="no_options" />
|
|
|
110 </options>
|
|
|
111 </param>
|
|
|
112 </when>
|
|
|
113 </conditional>
|
|
|
114 </xml>
|
|
|
115
|
|
|
116
|
|
|
117 <token name="@ADDTHREADS@"><![CDATA[
|
|
|
118 ##compute the number of ADDITIONAL threads to be used by samtools (-@)
|
|
|
119 addthreads=\${GALAXY_SLOTS:-1} && (( addthreads-- )) &&
|
|
|
120 ]]></token>
|
|
|
121 <token name="@ADDMEMORY@"><![CDATA[
|
|
|
122 ##compute the number of memory available to samtools sort (-m)
|
|
|
123 ##use only 75% of available: https://github.com/samtools/samtools/issues/831
|
|
|
124 addmemory=\${GALAXY_MEMORY_MB_PER_SLOT:-768} &&
|
|
|
125 ((addmemory=addmemory*75/100)) &&
|
|
|
126 ]]></token>
|
|
|
127 <xml name="seed_input">
|
|
|
128 <param name="seed" type="integer" optional="True" label="Seed for random number generator" help="If empty a random seed is used." />
|
|
|
129 </xml>
|
|
|
130 <xml name="flag_options" token_s1="false" token_s2="false" token_s4="false" token_s8="false" token_s16="false" token_s32="false" token_s64="false" token_s128="false" token_s256="false" token_s512="false" token_s1024="false" token_s2048="false">
|
|
|
131 <option value="1" selected="@S1@">Read is paired</option>
|
|
|
132 <option value="2" selected="@S2@">Read is mapped in a proper pair</option>
|
|
|
133 <option value="4" selected="@S4@">Read is unmapped</option>
|
|
|
134 <option value="8" selected="@S8@">Mate is unmapped</option>
|
|
|
135 <option value="16" selected="@S16@">Read is mapped to the reverse strand of the reference</option>
|
|
|
136 <option value="32" selected="@S32@">Mate is mapped to the reverse strand of the reference</option>
|
|
|
137 <option value="64" selected="@S64@">Read is the first in a pair</option>
|
|
|
138 <option value="128" selected="@S128@">Read is the second in a pair</option>
|
|
|
139 <option value="256" selected="@S256@">Alignment of the read is not primary</option>
|
|
|
140 <option value="512" selected="@S512@">Read fails platform/vendor quality checks</option>
|
|
|
141 <option value="1024" selected="@S1024@">Read is a PCR or optical duplicate</option>
|
|
|
142 <option value="2048" selected="@S2048@">Alignment is supplementary</option>
|
|
|
143 </xml>
|
|
|
144
|
|
|
145 <!-- region specification macros and tokens for tools that allow the specification
|
|
|
146 of region by bed file / space separated list of regions -->
|
|
|
147 <token name="@REGIONS_FILE@"><![CDATA[
|
|
|
148 #if $cond_region.select_region == 'tab':
|
|
|
149 -t '$cond_region.targetregions'
|
|
|
150 #end if
|
|
|
151 ]]></token>
|
|
|
152 <token name="@REGIONS_MANUAL@"><![CDATA[
|
|
|
153 #if $cond_region.select_region == 'text':
|
|
|
154 #for $i, $x in enumerate($cond_region.regions_repeat):
|
|
|
155 '${x.region}'
|
|
|
156 #end for
|
|
|
157 #end if
|
|
|
158 ]]></token>
|
|
|
159 <xml name="regions_macro">
|
|
|
160 <conditional name="cond_region">
|
|
|
161 <param name="select_region" type="select" label="Filter by regions" help="restricts output to only those alignments which overlap the specified region(s)">
|
|
|
162 <option value="no" selected="True">No</option>
|
|
|
163 <option value="text">Manualy specify regions</option>
|
|
|
164 <option value="tab">Regions from tabular file</option>
|
|
|
165 </param>
|
|
|
166 <when value="no"/>
|
|
|
167 <when value="text">
|
|
|
168 <repeat name="regions_repeat" min="1" default="1" title="Regions">
|
|
|
169 <param name="region" type="text" label="region" help="format chr:from-to">
|
|
|
170 <validator type="regex" message="Required format: CHR[:FROM[-TO]]; where CHR: string containing any character except quotes, whitespace and colon; FROM and TO: any integer">^[^\s'\":]+(:\d+(-\d+){0,1}){0,1}$</validator>
|
|
|
171 </param>
|
|
|
172 </repeat>
|
|
|
173 </when>
|
|
|
174 <when value="tab">
|
|
|
175 <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)" />
|
|
|
176 </when>
|
|
|
177 </conditional>
|
|
|
178 </xml>
|
|
|
179
|
|
|
180 <xml name="citations">
|
|
|
181 <citations>
|
|
|
182 <citation type="bibtex">
|
|
|
183 @misc{SAM_def,
|
|
|
184 title={Definition of SAM/BAM format},
|
|
|
185 url = {https://samtools.github.io/hts-specs/},}
|
|
|
186 </citation>
|
|
|
187 <citation type="doi">10.1093/bioinformatics/btp352</citation>
|
|
|
188 <citation type="doi">10.1093/bioinformatics/btr076</citation>
|
|
|
189 <citation type="doi">10.1093/bioinformatics/btr509</citation>
|
|
|
190 <citation type="bibtex">
|
|
|
191 @misc{Danecek_et_al,
|
|
|
192 Author={Danecek, P., Schiffels, S., Durbin, R.},
|
|
|
193 title={Multiallelic calling model in bcftools (-m)},
|
|
|
194 url = {http://samtools.github.io/bcftools/call-m.pdf},}
|
|
|
195 </citation>
|
|
|
196 <citation type="bibtex">
|
|
|
197 @misc{Durbin_VCQC,
|
|
|
198 Author={Durbin, R.},
|
|
|
199 title={Segregation based metric for variant call QC},
|
|
|
200 url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},}
|
|
|
201 </citation>
|
|
|
202 <citation type="bibtex">
|
|
|
203 @misc{Li_SamMath,
|
|
|
204 Author={Li, H.},
|
|
|
205 title={Mathematical Notes on SAMtools Algorithms},
|
|
|
206 url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},}
|
|
|
207 </citation>
|
|
|
208 <citation type="bibtex">
|
|
|
209 @misc{SamTools_github,
|
|
|
210 title={SAMTools GitHub page},
|
|
|
211 url = {https://github.com/samtools/samtools},}
|
|
|
212 </citation>
|
|
|
213 </citations>
|
|
|
214 </xml>
|
|
|
215 <xml name="version_command">
|
|
|
216 <version_command><![CDATA[samtools 2>&1 | grep Version]]></version_command>
|
|
|
217 </xml>
|
|
|
218 <xml name="stdio">
|
|
|
219 <stdio>
|
|
|
220 <exit_code range="1:" level="fatal" description="Error" />
|
|
|
221 </stdio>
|
|
|
222 </xml>
|
|
|
223 </macros>
|
