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comparison lofreq_call.xml @ 2:dfadc322b065 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729"
author iuc
date Wed, 12 Feb 2020 18:45:42 -0500
parents 31216d510164
children 3b4b2121842f
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1:03627f24605f 2:dfadc322b065
1 <tool id="lofreq_call" name="Call variants" version="@WRAPPER_VERSION@0"> 1 <tool id="lofreq_call" name="Call variants" version="@TOOL_VERSION@+galaxy1">
2 <description>with LoFreq</description> 2 <description>with LoFreq</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 ## prepare reference genome and mapped reads input 8 ## prepare reference genome and mapped reads input
9 @PREPARE_REF@ 9 @PREPARE_REF@
10 ln -s '$reads' reads.bam && 10 ln -s '$reads' reads.bam &&
11 ln -s -f '${reads.metadata.bam_index}' reads.bam.bai && 11 ln -s -f '${reads.metadata.bam_index}' reads.bam.bai &&
12 #if str($call_control.set_call_options) == 'yes':
13 #set $ign_vcfs = []
14 #if str($call_control.source_qual.use_src_qual.src_qual):
15 #for $n, $ign_vcf in enumerate($call_control.source_qual.use_src_qual.ign_vcf):
16 ## lofreq recognizes compressed vcf input based on its .gz
17 ## suffix => symlink all datasets with standard extensions.
18 ## For bgzipped vcfs, also make the index files available.
19 #if $ign_vcf:
20 #if $ign_vcf.is_of_type('vcf_bgzip'):
21 #set $ign_src = 'ign%d.vcf.gz' % $n
22 ln -s '$ign_vcf' $ign_src &&
23 ln -s '$ign_vcf.metadata.tabix_index' ${ign_src}.tbi &&
24 #else:
25 #set $ign_src = 'ign%d.vcf' % $n
26 ln -s '$ign_vcf' $ign_src &&
27 #end if
28 #silent $ign_vcfs.append($ign_src)
29 #end if
30 #end for
31 #end if
32 #set $ign_vcfs = ','.join($ign_vcfs)
33 #end if
12 34
13 ## call variants with lofreq 35 ## call variants with lofreq
14 36
15 ## make lofreq stick to tool contract by 37 ## make lofreq stick to tool contract by
16 ## generating tmp output inside job working dir 38 ## generating tmp output inside job working dir
28 #if str($call_control.set_call_options) == 'yes': 50 #if str($call_control.set_call_options) == 'yes':
29 --min-cov $call_control.coverage.min_cov 51 --min-cov $call_control.coverage.min_cov
30 --max-depth $call_control.coverage.max_depth 52 --max-depth $call_control.coverage.max_depth
31 $call_control.pe.use_orphan 53 $call_control.pe.use_orphan
32 --min-bq $call_control.bc_quals.min_bq 54 --min-bq $call_control.bc_quals.min_bq
33 --min-alt-bq $call_control.bc_quals.min_alt_bq 55 #if $call_control.bc_quals.min_alt_bq > $call_control.bc_quals.min_bq:
34 --def-alt-bq $call_control.bc_quals.def_alt_bq 56 --min-alt-bq $call_control.bc_quals.min_alt_bq
57 #else:
58 --min-alt-bq $call_control.bc_quals.min_bq
59 #end if
60 #if str($call_control.bc_quals.alt_bq.modify):
61 --def-alt-bq $call_control.bc_quals.alt_bq.def_alt_bq
62 #end if
35 ${call_control.align_quals.alnqual.use_alnqual} 63 ${call_control.align_quals.alnqual.use_alnqual}
36 #if str($call_control.align_quals.alnqual.use_alnqual) != '-A -B': 64 #if str($call_control.align_quals.alnqual.use_alnqual) != '-A -B':
37 ${call_control.align_quals.alnqual.alnqual_choice.alnquals_to_use} 65 ${call_control.align_quals.alnqual.alnqual_choice.alnquals_to_use}
38 ${call_control.align_quals.alnqual.alnqual_choice.extended_baq} 66 ${call_control.align_quals.alnqual.alnqual_choice.extended_baq}
39 #end if 67 #end if
40 --min-mq $call_control.map_quals.min_mq 68 --min-mq $call_control.map_quals.min_mq
41 --max-mq $call_control.map_quals.use_mq.max_mq 69 #if str($call_control.map_quals.use_mq.no_mq):
42 $call_control.map_quals.use_mq.no_mq 70 $call_control.map_quals.use_mq.no_mq
71 #else:
72 #if $call_control.map_quals.use_mq.max_mq > $call_control.map_quals.min_mq:
73 --max-mq $call_control.map_quals.use_mq.max_mq
74 #else:
75 --max-mq $call_control.map_quals.min_mq
76 #end if
77 #end if
43 #if str($call_control.source_qual.use_src_qual.src_qual): 78 #if str($call_control.source_qual.use_src_qual.src_qual):
44 $call_control.source_qual.use_src_qual.src_qual 79 $call_control.source_qual.use_src_qual.src_qual
45 #set $ign_vcfs = ','.join([str($ign_vcf) for $ign_vcf in $call_control.source_qual.use_src_qual.ign_vcf if $ign_vcf])
46 #if $ign_vcfs: 80 #if $ign_vcfs:
47 --ign-vcf "$ign_vcfs" 81 --ign-vcf '$ign_vcfs'
48 #end if 82 #end if
49 --def-nm-q $call_control.source_qual.use_src_qual.def_nm_q 83 --def-nm-q $call_control.source_qual.use_src_qual.def_nm_q
50 #end if 84 #end if
51 --min-jq $call_control.joint_qual.min_jq 85 --min-jq $call_control.joint_qual.min_jq
52 --min-alt-jq $call_control.joint_qual.min_alt_jq 86 --min-alt-jq $call_control.joint_qual.min_alt_jq
123 label="Minimum baseQ" 157 label="Minimum baseQ"
124 help="For variant calling at any given site, do not consider reads for which the base at that site has a base quality less than this value (default: 6)" /> 158 help="For variant calling at any given site, do not consider reads for which the base at that site has a base quality less than this value (default: 6)" />
125 <param name="min_alt_bq" argument="--min-alt-bq" type="integer" min="0" value="6" 159 <param name="min_alt_bq" argument="--min-alt-bq" type="integer" min="0" value="6"
126 label="Minimum baseQ for alternate bases" 160 label="Minimum baseQ for alternate bases"
127 help="For variant calling at any given site, do not consider reads that support a non-reference allele at the site if that base has a base quality less than this value (default: 6). Note: this setting will have no effect if the specified value is less than the general Minimum baseQ above." /> 161 help="For variant calling at any given site, do not consider reads that support a non-reference allele at the site if that base has a base quality less than this value (default: 6). Note: this setting will have no effect if the specified value is less than the general Minimum baseQ above." />
128 <param name="def_alt_bq" argument="--def-alt-bq" type="integer" min="0" value="0" 162 <conditional name="alt_bq">
129 label="Overwrite baseQs of alternate bases with this value" 163 <param name="modify" type="select"
130 help="After filtering reads according to the Minimum baseQ settings above, set the base quality of the non-reference bases in the surviving reads to this new value (default: 0 = keep the original base quality)." /> 164 label="Base quality to use for alternate bases"
165 help="After filtering reads according to the Minimum baseQ settings above, you can choose to modify the base qualities of the non-reference bases in the surviving reads before performing further calculations.">
166 <option value="">Use original base qualities</option>
167 <option value="avg">Use the median of the reference base qualities at the site</option>
168 <option value="custom">Use a fixed custom value</option>
169 </param>
170 <when value="" />
171 <when value="avg">
172 <param name="def_alt_bq" type="hidden" value="-1" />
173 </when>
174 <when value="custom">
175 <param name="def_alt_bq" argument="--def-alt-bq" type="integer" min="1" value="1"
176 label="Overwrite original base qualities with this value" />
177 </when>
178 </conditional>
131 </section> 179 </section>
132 <section name="align_quals" title="Base alignment quality" expanded="true" 180 <section name="align_quals" title="Base alignment quality" expanded="true"
133 help="Choose here whether you want to incorporate base and/or indel alignment qualities into lofreq's joint quality model. If you have previously computed and stored (using lofreq alnqual) any of these quality scores into your input dataset, you can tell the tool to reuse them. Alternatively, the tool can calculate the necessary scores on the fly."> 181 help="Choose here whether you want to incorporate base and/or indel alignment qualities into lofreq's joint quality model. If you have previously computed and stored (using lofreq alnqual) any of these quality scores into your input dataset, you can tell the tool to reuse them. Alternatively, the tool can calculate the necessary scores on the fly.">
134 <conditional name="alnqual"> 182 <conditional name="alnqual">
135 <param name="use_alnqual" type="select" 183 <param name="use_alnqual" type="select"
158 <option value="--no-mq">No, ignore MAPQ scores during variant calling</option> 206 <option value="--no-mq">No, ignore MAPQ scores during variant calling</option>
159 </param> 207 </param>
160 <when value=""> 208 <when value="">
161 <param name="max_mq" argument="--max-mq" type="integer" value="255" 209 <param name="max_mq" argument="--max-mq" type="integer" value="255"
162 label="Maximum mapping quality" 210 label="Maximum mapping quality"
163 help="For the joint quality model at any site, cap the mapping quality of reads at this value (default: 255 = do not cap mapping qualities). Note: The special MAPQ value 255 is used by many tools to indicate undefined mapping quality, and lofreq call will ignore such reads during variant calling. Capping, however, will turn 255 into a regular MAPQ score. Thus, if you need to avoid using such reads, you should filter out MAPQ 255 reads from your input data with other tools before using lofreq call with MAPQ capping."/> 211 help="For the joint quality model at any site, cap the mapping quality of reads at this value (default: 255 = do not cap mapping qualities). Notes: 1) You cannot cap mapping qualities at less than the minimum MAPQ defined above. If you try, MAPQs will be capped at that minimum quality instead. 2) The special MAPQ value 255 is used by many tools to indicate undefined mapping quality, and lofreq call will ignore such reads during variant calling. Capping, however, will turn 255 into a regular MAPQ score. Thus, if you need to avoid using such reads, you should filter out MAPQ 255 reads from your input data with other tools before using lofreq call with MAPQ capping."/>
164 </when> 212 </when>
165 <when value="--no-mq"> 213 <when value="--no-mq">
166 <param name="max_mq" type="hidden" value="" /> 214 <param name="max_mq" type="hidden" value="" />
167 </when> 215 </when>
168 </conditional> 216 </conditional>
177 <when value="" /> 225 <when value="" />
178 <when value="--src-qual"> 226 <when value="--src-qual">
179 <param name="def_nm_q" argument="--def-nm-q" type="integer" min="-1" value="-1" 227 <param name="def_nm_q" argument="--def-nm-q" type="integer" min="-1" value="-1"
180 label="Replace non-match base qualities with this value" 228 label="Replace non-match base qualities with this value"
181 help="For the calculation of the source quality, replace all base qualities of non-match bases with this value (default: -1 = use original base qualities)." /> 229 help="For the calculation of the source quality, replace all base qualities of non-match bases with this value (default: -1 = use original base qualities)." />
182 <param name="ign_vcf" argument="--ign-vcf" type="data" format="vcf" optional="true" multiple="true" 230 <param name="ign_vcf" argument="--ign-vcf" type="data" format="vcf,vcf_bgzip" optional="true" multiple="true"
183 label="VCF input(s) with variants to ignore for source quality computation" 231 label="VCF input(s) with variants to ignore for source quality computation"
184 help="Mismatches caused by known true variants in your samples should not lower the source quality estimate. If any read in your input has a base that is non-reference, but supports one of the known variants in the specified VCF datasets, that base will not be treated as a mismatch." /> 232 help="Mismatches caused by known true variants in your samples should not lower the source quality estimate. If any read in your input has a base that is non-reference, but supports one of the known variants in the specified VCF datasets, that base will not be treated as a mismatch." />
185 </when> 233 </when>
186 </conditional> 234 </conditional>
187 </section> 235 </section>
240 <tests> 288 <tests>
241 <test> 289 <test>
242 <param name="reads" ftype="bam" value="lofreq-in1.bam" /> 290 <param name="reads" ftype="bam" value="lofreq-in1.bam" />
243 <param name="ref_selector" value="history" /> 291 <param name="ref_selector" value="history" />
244 <param name="ref" ftype="fasta" value="pBR322.fa" /> 292 <param name="ref" ftype="fasta" value="pBR322.fa" />
293 <output name="variants" file="call-out1.vcf" lines_diff="4" />
294 </test>
295 <test>
296 <param name="reads" ftype="bam" value="lofreq-in1.bam" />
297 <param name="ref_selector" value="history" />
298 <param name="ref" ftype="fasta" value="pBR322.fa" />
299 <conditional name="call_control">
300 <param name="set_call_options" value="yes" />
301 </conditional>
302 <output name="variants" file="call-out1.vcf" lines_diff="4" />
303 </test>
304 <test>
305 <param name="reads" ftype="bam" value="lofreq-in1.bam" />
306 <param name="ref_selector" value="history" />
307 <param name="ref" ftype="fasta" value="pBR322.fa" />
308 <conditional name="call_control">
309 <param name="set_call_options" value="yes" />
310 <section name="source_qual">
311 <conditional name="use_src_qual">
312 <param name="src_qual" value="--src-qual" />
313 <param name="def_nm_q" value="40" />
314 <param name="ign_vcf" ftype="vcf" value="call-out1.vcf" />
315 </conditional>
316 </section>
317 </conditional>
245 <output name="variants" file="call-out1.vcf" lines_diff="4" /> 318 <output name="variants" file="call-out1.vcf" lines_diff="4" />
246 </test> 319 </test>
247 <test> 320 <test>
248 <param name="reads" ftype="bam" value="lofreq-in1.bam" /> 321 <param name="reads" ftype="bam" value="lofreq-in1.bam" />
249 <param name="ref_selector" value="history" /> 322 <param name="ref_selector" value="history" />