Mercurial > repos > iuc > samtools_ampliconclip
comparison macros.xml @ 0:a941babb9268 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_ampliconclip commit 4596e7b08744df85b48d106cf4d44ebdd90dd554
author | iuc |
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date | Mon, 27 Jun 2022 20:07:59 +0000 |
parents | |
children | 5f3ea90dc6ae |
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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 ## Make the user-selected reference genome, if any, accessible through | |
54 ## a shell variable $reffa, index the reference if necessary, and make | |
55 ## the fai-index file available through a shell variable $reffai. | |
56 | |
57 ## For a cached genome simply sets the shell variables to point to the | |
58 ## genome file and its precalculated index. | |
59 ## For a genome from the user's history, if that genome is a plain | |
60 ## fasta file, the code creates a symlink in the pwd, creates the fai | |
61 ## index file next to it, then sets the shell variables to point to the | |
62 ## symlink and its index. | |
63 ## For a fasta.gz dataset from the user's history, it tries the same, | |
64 ## but this will only succeed if the file got compressed with bgzip. | |
65 ## For a regular gzipped file samtools faidx will fail, in which case | |
66 ## the code falls back to decompressing to plain fasta before | |
67 ## reattempting the indexing. | |
68 ## Indexing of a bgzipped file produces a regular fai index file *and* | |
69 ## a compressed gzi file. The former is identical to the fai index of | |
70 ## the uncompressed fasta. | |
71 | |
72 ## If the user has not selected a reference (it's an optional parameter | |
73 ## in some samtools wrappers), a cheetah boolean use_ref is set to | |
74 ## False to encode that fact. | |
75 | |
76 #set use_ref=True | |
77 #if $addref_cond.addref_select == "history": | |
78 #if $addref_cond.ref.is_of_type('fasta'): | |
79 reffa="reference.fa" && | |
80 ln -s '${addref_cond.ref}' \$reffa && | |
81 samtools faidx \$reffa && | |
82 #else: | |
83 reffa="reference.fa.gz" && | |
84 ln -s '${addref_cond.ref}' \$reffa && | |
85 { | |
86 samtools faidx \$reffa || | |
87 { | |
88 echo "Failed to index compressed reference. Trying decompressed ..." 1>&2 && | |
89 gzip -dc \$reffa > reference.fa && | |
90 reffa="reference.fa" && | |
91 samtools faidx \$reffa; | |
92 } | |
93 } && | |
94 #end if | |
95 reffai=\$reffa.fai && | |
96 #elif $addref_cond.addref_select == "cached": | |
97 ## in case of cached the absolute path is used which allows to read | |
98 ## a cram file without specifying the reference | |
99 reffa='${addref_cond.ref.fields.path}' && | |
100 reffai=\$reffa.fai && | |
101 #else | |
102 #set use_ref=False | |
103 #end if | |
104 ]]></token> | |
105 | |
106 <xml name="optional_reference"> | |
107 <conditional name="addref_cond"> | |
108 <param name="addref_select" type="select" label="Use a reference sequence"> | |
109 <help>@HELP@</help> | |
110 <option value="no">No</option> | |
111 <option value="history">Use a genome/index from the history</option> | |
112 <option value="cached">Use a built-in genome</option> | |
113 </param> | |
114 <when value="no"/> | |
115 <when value="history"> | |
116 <param name="ref" argument="@ARGUMENT@" type="data" format="fasta,fasta.gz" label="Reference"/> | |
117 </when> | |
118 <when value="cached"> | |
119 <param name="ref" argument="@ARGUMENT@" type="select" label="Reference"> | |
120 <options from_data_table="fasta_indexes"> | |
121 <filter type="data_meta" ref="input" key="dbkey" column="dbkey"/> | |
122 </options> | |
123 <validator type="no_options" message="No reference genome is available for the build associated with the selected input dataset"/> | |
124 </param> | |
125 </when> | |
126 </conditional> | |
127 </xml> | |
128 <xml name="mandatory_reference" token_help="" token_argument=""> | |
129 <conditional name="addref_cond"> | |
130 <param name="addref_select" type="select" label="Use a reference sequence"> | |
131 <help>@HELP@</help> | |
132 <option value="history">Use a genome/index from the history</option> | |
133 <option value="cached">Use a built-in genome</option> | |
134 </param> | |
135 <when value="history"> | |
136 <param name="ref" argument="@ARGUMENT@" type="data" format="fasta,fasta.gz" label="Reference"/> | |
137 </when> | |
138 <when value="cached"> | |
139 <param name="ref" argument="@ARGUMENT@" type="select" label="Reference"> | |
140 <options from_data_table="fasta_indexes"> | |
141 <filter type="data_meta" ref="input" key="dbkey" column="dbkey"/> | |
142 <validator message="No reference genome is available for the build associated with the selected input dataset" type="no_options" /> | |
143 </options> | |
144 </param> | |
145 </when> | |
146 </conditional> | |
147 </xml> | |
148 | |
149 | |
150 <token name="@ADDTHREADS@"><![CDATA[ | |
151 ##compute the number of ADDITIONAL threads to be used by samtools (-@) | |
152 addthreads=\${GALAXY_SLOTS:-1} && (( addthreads-- )) && | |
153 ]]></token> | |
154 <token name="@ADDMEMORY@"><![CDATA[ | |
155 ##compute the number of memory available to samtools sort (-m) | |
156 ##use only 75% of available: https://github.com/samtools/samtools/issues/831 | |
157 addmemory=\${GALAXY_MEMORY_MB_PER_SLOT:-768} && | |
158 ((addmemory=addmemory*75/100)) && | |
159 ]]></token> | |
160 <xml name="seed_input"> | |
161 <param name="seed" type="integer" optional="True" label="Seed for random number generator" help="If empty a random seed is used." /> | |
162 </xml> | |
163 <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"> | |
164 <option value="1" selected="@S1@">Read is paired</option> | |
165 <option value="2" selected="@S2@">Read is mapped in a proper pair</option> | |
166 <option value="4" selected="@S4@">Read is unmapped</option> | |
167 <option value="8" selected="@S8@">Mate is unmapped</option> | |
168 <option value="16" selected="@S16@">Read is mapped to the reverse strand of the reference</option> | |
169 <option value="32" selected="@S32@">Mate is mapped to the reverse strand of the reference</option> | |
170 <option value="64" selected="@S64@">Read is the first in a pair</option> | |
171 <option value="128" selected="@S128@">Read is the second in a pair</option> | |
172 <option value="256" selected="@S256@">Alignment of the read is not primary</option> | |
173 <option value="512" selected="@S512@">Read fails platform/vendor quality checks</option> | |
174 <option value="1024" selected="@S1024@">Read is a PCR or optical duplicate</option> | |
175 <option value="2048" selected="@S2048@">Alignment is supplementary</option> | |
176 </xml> | |
177 | |
178 <!-- region specification macros and tokens for tools that allow the specification | |
179 of region by bed file / space separated list of regions --> | |
180 <token name="@REGIONS_FILE@"><![CDATA[ | |
181 #if $cond_region.select_region == 'tab': | |
182 -t '$cond_region.targetregions' | |
183 #end if | |
184 ]]></token> | |
185 <token name="@REGIONS_MANUAL@"><![CDATA[ | |
186 #if $cond_region.select_region == 'text': | |
187 #for $i, $x in enumerate($cond_region.regions_repeat): | |
188 '${x.region}' | |
189 #end for | |
190 #end if | |
191 ]]></token> | |
192 <xml name="regions_macro"> | |
193 <conditional name="cond_region"> | |
194 <param name="select_region" type="select" label="Filter by regions" help="restricts output to only those alignments which overlap the specified region(s)"> | |
195 <option value="no" selected="True">No</option> | |
196 <option value="text">Manualy specify regions</option> | |
197 <option value="tab">Regions from tabular file</option> | |
198 </param> | |
199 <when value="no"/> | |
200 <when value="text"> | |
201 <repeat name="regions_repeat" min="1" default="1" title="Regions"> | |
202 <param name="region" type="text" label="region" help="format chr:from-to"> | |
203 <validator type="regex" message="Required format: CHR[:FROM[-TO]]; where CHR: string containing any character except quotes, whitespace and colon; FROM and TO: any integer">^[^\s'\":]+(:\d+(-\d+){0,1}){0,1}$</validator> | |
204 </param> | |
205 </repeat> | |
206 </when> | |
207 <when value="tab"> | |
208 <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)" /> | |
209 </when> | |
210 </conditional> | |
211 </xml> | |
212 | |
213 <xml name="citations"> | |
214 <citations> | |
215 <citation type="bibtex"> | |
216 @misc{SAM_def, | |
217 title={Definition of SAM/BAM format}, | |
218 url = {https://samtools.github.io/hts-specs/},} | |
219 </citation> | |
220 <citation type="doi">10.1093/bioinformatics/btp352</citation> | |
221 <citation type="doi">10.1093/bioinformatics/btr076</citation> | |
222 <citation type="doi">10.1093/bioinformatics/btr509</citation> | |
223 <citation type="bibtex"> | |
224 @misc{Danecek_et_al, | |
225 Author={Danecek, P., Schiffels, S., Durbin, R.}, | |
226 title={Multiallelic calling model in bcftools (-m)}, | |
227 url = {http://samtools.github.io/bcftools/call-m.pdf},} | |
228 </citation> | |
229 <citation type="bibtex"> | |
230 @misc{Durbin_VCQC, | |
231 Author={Durbin, R.}, | |
232 title={Segregation based metric for variant call QC}, | |
233 url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},} | |
234 </citation> | |
235 <citation type="bibtex"> | |
236 @misc{Li_SamMath, | |
237 Author={Li, H.}, | |
238 title={Mathematical Notes on SAMtools Algorithms}, | |
239 url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},} | |
240 </citation> | |
241 <citation type="bibtex"> | |
242 @misc{SamTools_github, | |
243 title={SAMTools GitHub page}, | |
244 url = {https://github.com/samtools/samtools},} | |
245 </citation> | |
246 </citations> | |
247 </xml> | |
248 <xml name="version_command"> | |
249 <version_command><![CDATA[samtools 2>&1 | grep Version]]></version_command> | |
250 </xml> | |
251 <xml name="stdio"> | |
252 <stdio> | |
253 <exit_code range="1:" level="fatal" description="Error" /> | |
254 </stdio> | |
255 </xml> | |
256 </macros> |