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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
author iuc
date Sun, 08 Sep 2024 03:23:27 +0000
parents cf4d627c5cc0
children
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13:cf4d627c5cc0 14:43f90a79608d
3 <requirements> 3 <requirements>
4 <requirement type="package" version="@TOOL_VERSION@">samtools</requirement> 4 <requirement type="package" version="@TOOL_VERSION@">samtools</requirement>
5 <yield/> 5 <yield/>
6 </requirements> 6 </requirements>
7 </xml> 7 </xml>
8 <token name="@TOOL_VERSION@">1.13</token> 8 <!-- NOTE: for some tools only the version of the requirement but not the
9 <token name="@PROFILE@">20.05</token> 9 tool's version is controlled by the TOOL_VERSION token
10 (because their version is ahead of the requirement version ..
11 please only bump the minor version in order to let the requirement
12 version catch up eventually). To find the tools check:
13 `grep "<tool" . -r | grep -v VERSION_SUFFIX | cut -d":" -f 1` -->
14 <token name="@TOOL_VERSION@">1.20</token>
15 <token name="@VERSION_SUFFIX@">2</token>
16 <token name="@PROFILE@">22.05</token>
10 <token name="@FLAGS@"><![CDATA[ 17 <token name="@FLAGS@"><![CDATA[
11 #set $flags = 0 18 #set $flags = 0
12 #if $filter 19 #if $filter
13 #set $flags = sum(map(int, str($filter).split(','))) 20 #set $flags = sum(map(int, str($filter).split(',')))
14 #end if 21 #end if
48 #end if 55 #end if
49 #end if 56 #end if
50 #end for 57 #end for
51 ]]></token> 58 ]]></token>
52 <token name="@PREPARE_FASTA_IDX@"><![CDATA[ 59 <token name="@PREPARE_FASTA_IDX@"><![CDATA[
53 ##checks for reference data ($addref_cond.addref_select=="history" or =="cached") 60 ## Make the user-selected reference genome, if any, accessible through
54 ##and sets the -t/-T parameters accordingly: 61 ## a shell variable $reffa, index the reference if necessary, and make
55 ##- in case of history a symbolic link is used because samtools (view) will generate 62 ## the fai-index file available through a shell variable $reffai.
56 ## the index which might not be possible in the directory containing the fasta file 63
57 ##- in case of cached the absolute path is used which allows to read the cram file 64 ## For a cached genome simply sets the shell variables to point to the
58 ## without specifying the reference 65 ## genome file and its precalculated index.
66 ## For a genome from the user's history, if that genome is a plain
67 ## fasta file, the code creates a symlink in the pwd, creates the fai
68 ## index file next to it, then sets the shell variables to point to the
69 ## symlink and its index.
70 ## For a fasta.gz dataset from the user's history, it tries the same,
71 ## but this will only succeed if the file got compressed with bgzip.
72 ## For a regular gzipped file samtools faidx will fail, in which case
73 ## the code falls back to decompressing to plain fasta before
74 ## reattempting the indexing.
75 ## Indexing of a bgzipped file produces a regular fai index file *and*
76 ## a compressed gzi file. The former is identical to the fai index of
77 ## the uncompressed fasta.
78
79 ## If the user has not selected a reference (it's an optional parameter
80 ## in some samtools wrappers), a cheetah boolean use_ref is set to
81 ## False to encode that fact.
82
83 #set use_ref=True
59 #if $addref_cond.addref_select == "history": 84 #if $addref_cond.addref_select == "history":
60 ln -s '${addref_cond.ref}' reference.fa && 85 #if $addref_cond.ref.is_of_type('fasta'):
61 samtools faidx reference.fa && 86 reffa="reference.fa" &&
62 #set reffa="reference.fa" 87 ln -s '${addref_cond.ref}' \$reffa &&
63 #set reffai="reference.fa.fai" 88 samtools faidx \$reffa &&
89 #else:
90 reffa="reference.fa.gz" &&
91 ln -s '${addref_cond.ref}' \$reffa &&
92 {
93 samtools faidx \$reffa ||
94 {
95 echo "Failed to index compressed reference. Trying decompressed ..." 1>&2 &&
96 gzip -dc \$reffa > reference.fa &&
97 reffa="reference.fa" &&
98 samtools faidx \$reffa;
99 }
100 } &&
101 #end if
102 reffai=\$reffa.fai &&
64 #elif $addref_cond.addref_select == "cached": 103 #elif $addref_cond.addref_select == "cached":
65 #set reffa=str($addref_cond.ref.fields.path) 104 ## in case of cached the absolute path is used which allows to read
66 #set reffai=str($addref_cond.ref.fields.path)+".fai" 105 ## a cram file without specifying the reference
106 reffa='${addref_cond.ref.fields.path}' &&
107 reffai=\$reffa.fai &&
67 #else 108 #else
68 #set reffa=None 109 #set use_ref=False
69 #set reffai=None 110 #end if
70 #end if 111 ]]></token>
71 ]]></token> 112
72 113 <xml name="optional_reference" token_help="" token_argument="">
73 <xml name="optional_reference">
74 <conditional name="addref_cond"> 114 <conditional name="addref_cond">
75 <param name="addref_select" type="select" label="Use a reference sequence"> 115 <param name="addref_select" type="select" label="Use a reference sequence">
76 <help>@HELP@</help> 116 <help>@HELP@</help>
77 <option value="no">No</option> 117 <option value="no">No</option>
78 <option value="history">Use a genome/index from the history</option> 118 <option value="history">Use a genome/index from the history</option>
177 </conditional> 217 </conditional>
178 </xml> 218 </xml>
179 219
180 <xml name="citations"> 220 <xml name="citations">
181 <citations> 221 <citations>
182 <citation type="bibtex"> 222 <citation type="doi">10.1093/gigascience/giab008</citation>
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> 223 </citations>
214 </xml> 224 </xml>
215 <xml name="version_command"> 225 <xml name="version_command">
216 <version_command><![CDATA[samtools 2>&1 | grep Version]]></version_command> 226 <version_command><![CDATA[samtools 2>&1 | grep Version]]></version_command>
217 </xml> 227 </xml>