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comparison samtools_view.xml @ 2:80d8ca44f8da draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1047dc0e36a1c28492d7cd1e860c89ecf3ba30c8
author iuc
date Thu, 27 Sep 2018 08:49:45 -0400
parents 390fc279c3e5
children 097c44aaf6d4
comparison
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1:390fc279c3e5 2:80d8ca44f8da
1 <tool id="samtools_view" name="Samtools view" version="@TOOL_VERSION@"> 1 <tool id="samtools_view" name="Samtools view" version="@TOOL_VERSION@">
2 <description>reformat, filter, or subsample</description> 2 <description>reformat, filter, or subsample</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 <requirement type="package">gawk</requirement>
8 </expand>
7 <expand macro="stdio"/> 9 <expand macro="stdio"/>
8 <expand macro="version_command"/> 10 <expand macro="version_command"/>
9 <command><![CDATA[ 11 <command><![CDATA[
10 @ADDTHREADS@ 12 @ADDTHREADS@
11 ## prepare reference data 13 ## prepare reference data
12 @PREPARE_FASTA_IDX@ 14 @PREPARE_FASTA_IDX@
13 @PREPARE_IDX@ 15 @PREPARE_IDX@
14 16 #if $cond_subsample.select_subsample == 'target':
17 ##this must be done before the main command because we don't know the total # reads until execution time
18 #if str($cond_subsample.seed) == '':
19 #set seed_expr="int(rand() * 32768)"
20 #else
21 #set seed_expr=$cond_subsample.seed
22 #end if
23 #if $input.is_of_type('sam'):
24 sample_fragment=`samtools view -c infile | awk '{s=\$1} END {frac=$cond_subsample.target/s; print(frac < 1 ? "-s " $seed_expr+frac : "")}'` &&
25 #else
26 sample_fragment=`samtools idxstats infile | awk '{s+=\$4+\$3} END {frac=$cond_subsample.target/s; print(frac < 1 ? "-s " $seed_expr+frac : "")}'` &&
27 #end if
28 #end if
15 ##call samtools view 29 ##call samtools view
16 samtools view 30 samtools view
17 -@ \$addthreads 31 -@ \$addthreads
18 32
19 #if $outtype == 'count': 33 #if $outtype == 'count':
60 #end if 74 #end if
61 #for $i, $s in enumerate($cond_filter.readtags) 75 #for $i, $s in enumerate($cond_filter.readtags)
62 -x '${s.readtag}' 76 -x '${s.readtag}'
63 #end for 77 #end for
64 #end if 78 #end if
65 #if $cond_subsample.select_subsample == 'yes': 79 #if $cond_subsample.select_subsample != 'no':
66 #set fraction=str($cond_subsample.subsample).split('.')[1] 80 #if $cond_subsample.select_subsample == "target":
67 #if str($cond_subsample.seed) == '': 81 ##this is calculated at execution time before the main samtools command
68 -s "\${RANDOM}".$fraction 82 "\${sample_fragment}"
69 #else 83 #else
70 -s $cond_subsample.seed.$fraction 84 #set fraction=str($cond_subsample.fraction).split('.')[1]
85 #if str($cond_subsample.seed) == '':
86 -s "\${RANDOM}".$fraction
87 #else
88 -s $cond_subsample.seed.$fraction
89 #end if
71 #end if 90 #end if
72 #end if 91 #end if
73 92
74 ## output options 93 ## output options
75 $adv_output.header 94 $adv_output.header
179 </when> 198 </when>
180 <when value="no"/> 199 <when value="no"/>
181 </conditional> 200 </conditional>
182 <conditional name="cond_subsample"> 201 <conditional name="cond_subsample">
183 <param name="select_subsample" type="select" argument="-s" label="Subsample alignment"> 202 <param name="select_subsample" type="select" argument="-s" label="Subsample alignment">
184 <option value="yes">Yes</option> 203 <option value="fraction">Specify a fraction to keep</option>
185 <option value="no" selected="True">No</option> 204 <option value="target">Specify a target # of reads</option>
205 <option value="no" selected="True">No downsampling</option>
186 </param> 206 </param>
187 <when value="yes"> 207 <when value="fraction">
188 <param name="subsample" type="float" optional="False" value="0.5" min="0" max="1" label="Subsampling fraction" help="sets the fraction of templates/pairs to subsample." /> 208 <param name="fraction" type="float" optional="False" value="0.5" min="0" max="1" label="Subsampling fraction" help="sets the fraction of templates/pairs to subsample." />
189 <param name="seed" type="integer" optional="True" label="Seed for random number generator" help="If empty a random seed is used." /> 209 <expand macro="seed_input" />
210 </when>
211 <when value='target'>
212 <param name="target" type="integer" optional="False" value="" min="0" label="Target # of reads" help="sets the target number of reads to subsample." />
213 <expand macro="seed_input" />
190 </when> 214 </when>
191 <when value="no"/> 215 <when value="no"/>
192 </conditional> 216 </conditional>
193 <conditional name="addref_cond"> 217 <conditional name="addref_cond">
194 <param name="addref_select" type="select" label="Reference data"> 218 <param name="addref_select" type="select" label="Reference data">
381 <conditional name="cond_region"> 405 <conditional name="cond_region">
382 <param name="select_region" value="no"/> 406 <param name="select_region" value="no"/>
383 </conditional> 407 </conditional>
384 <output name="outputsam" file="sam_to_bam_out2.bam" ftype="bam" /> 408 <output name="outputsam" file="sam_to_bam_out2.bam" ftype="bam" />
385 </test> 409 </test>
410 <!-- sampling options-->
411 <test>
412 <param name="input" value="test.sam" ftype="sam" />
413 <param name="outtype" value="sam" />
414 <conditional name="cond_subsample">
415 <param name="select_subsample" value="target" />
416 <param name="target" value="2" />
417 </conditional>
418 <output name="outputsam" file="test_ds.sam" ftype="sam" compare="diff" lines_diff="6" />
419 </test>
420 <test>
421 <param name="input" value="test.sam" ftype="sam" />
422 <param name="outtype" value="sam" />
423 <conditional name="cond_subsample">
424 <param name="select_subsample" value="target" />
425 <param name="seed" value="7" />
426 <param name="target" value="2" />
427 </conditional>
428 <output name="outputsam" file="test_ds.sam" ftype="sam" compare="diff" lines_diff="4" />
429 </test>
430 <test>
431 <param name="input" value="test.bam" ftype="bam" />
432 <param name="outtype" value="bam" />
433 <conditional name="cond_subsample">
434 <param name="select_subsample" value="target" />
435 <param name="seed" value="7" />
436 <param name="target" value="2" />
437 </conditional>
438 <output name="outputsam" file="test_ds.bam" ftype="bam" />
439 </test>
440 <test>
441 <param name="input" value="test.bam" ftype="bam" />
442 <param name="outtype" value="bam" />
443 <conditional name="cond_subsample">
444 <param name="select_subsample" value="fraction" />
445 <param name="seed" value="7" />
446 <param name="fraction" value=".2" />
447 </conditional>
448 <output name="outputsam" file="test_ds.bam" ftype="bam" />
449 </test>
386 </tests> 450 </tests>
387 <help> 451 <help>
388 **What it does** 452 **What it does**
389 453
390 Samtools view can: 454 Samtools view can: