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comparison ivar_trim.xml @ 2:cb903c9dc33d draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 2d91c217cf30938da84dea51aa3c45a7789db0fc"
author iuc
date Wed, 22 Apr 2020 06:05:42 -0400
parents 8858fa037a15
children 5d6ed46cc101
comparison
equal deleted inserted replaced
1:d37ede8589b2 2:cb903c9dc33d
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <expand macro="version_command" /> 7 <expand macro="version_command" />
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 ln -s '$input_bed' bed.bed && 9 #if $primer.source == "history"
10 ln -s '$primer.input_bed' bed.bed &&
11 #else
12 ln -s '$primer.cached_bed.fields.path' bed.bed &&
13 #end if
10 ln -s '$input_bam' sorted.bam && 14 ln -s '$input_bam' sorted.bam &&
11 ivar trim 15 ivar trim
12 -i sorted.bam 16 -i sorted.bam
13 -b bed.bed 17 -b bed.bed
14 -m $min_len 18 -m $min_len
19 samtools sort -@ \${GALAXY_SLOTS:-1} -o trimmed.sorted.bam trimmed.bam && 23 samtools sort -@ \${GALAXY_SLOTS:-1} -o trimmed.sorted.bam trimmed.bam &&
20 samtools index -@ \${GALAXY_SLOTS:-1} trimmed.sorted.bam 24 samtools index -@ \${GALAXY_SLOTS:-1} trimmed.sorted.bam
21 ]]> </command> 25 ]]> </command>
22 <inputs> 26 <inputs>
23 <param name="input_bam" argument="-i" type="data" format="bam" label="Bam file" help="Aligned reads, to trim primers and quality"/> 27 <param name="input_bam" argument="-i" type="data" format="bam" label="Bam file" help="Aligned reads, to trim primers and quality"/>
24 <param name="input_bed" argument="-b" type="data" format="bed" label="BED file with primer sequences and positions"/> 28 <conditional name="primer">
29 <param label="Source of primer information" name="source" type="select">
30 <option value="history" selected="true">History</option>
31 <option value="cached">Built-in</option>
32 </param>
33 <when value="history">
34 <param name="input_bed" argument="-b" type="data" format="bed" label="BED file with primer sequences and positions"/>
35 </when>
36 <when value="cached">
37 <param name="cached_bed" type="select" label="Primer scheme name" help="Select primer scheme bed file from a list">
38 <options from_data_table="primer_scheme_bedfiles">
39 <filter type="sort_by" column="1" />
40 <validator type="no_options" message="No primer schemes are available" />
41 </options>
42 </param>
43 </when>
44 </conditional>
25 <param name="min_len" argument="-m" type="integer" min="0" value="30" label="Minimum length of read to retain after trimming"/> 45 <param name="min_len" argument="-m" type="integer" min="0" value="30" label="Minimum length of read to retain after trimming"/>
26 <param name="min_qual" argument="-q" type="integer" min="0" value="20" label="Minimum quality threshold for sliding window to pass"/> 46 <param name="min_qual" argument="-q" type="integer" min="0" value="20" label="Minimum quality threshold for sliding window to pass"/>
27 <param name="window_width" argument="-s" type="integer" min="0" value="4" label="Width of sliding window"/> 47 <param name="window_width" argument="-s" type="integer" min="0" value="4" label="Width of sliding window"/>
28 <param name="inc_primers" argument="-e" type="boolean" truevalue="-e" falsevalue="" checked="false" label="Include reads with no primers"/> 48 <param name="inc_primers" argument="-e" type="boolean" truevalue="-e" falsevalue="" checked="false" label="Include reads with no primers"/>
29 </inputs> 49 </inputs>
38 <param name="inc_primers" value="true" /> 58 <param name="inc_primers" value="true" />
39 <output name="output_bam" file="covid19/PC00101P_sub.sorted.bam" compare="sim_size" delta="300000"/> 59 <output name="output_bam" file="covid19/PC00101P_sub.sorted.bam" compare="sim_size" delta="300000"/>
40 </test> 60 </test>
41 <!-- #1: Zika data--> 61 <!-- #1: Zika data-->
42 <test> 62 <test>
63 <conditional name="primer">
64 <param name="source" value="history" />
65 <param name="input_bed" value="zika/db/zika_primers.bed" />
66 </conditional>
43 <param name="input_bam" value="zika/Z52_a.sorted.bam" /> 67 <param name="input_bam" value="zika/Z52_a.sorted.bam" />
44 <param name="input_bed" value="zika/db/zika_primers.bed" />
45 <output name="output_bam" file="zika/Z52_a.trimmed.sorted.bam" compare="sim_size" delta="100000"/> 68 <output name="output_bam" file="zika/Z52_a.trimmed.sorted.bam" compare="sim_size" delta="100000"/>
46 </test> 69 </test>
47 <test> 70 <test>
71 <conditional name="primer">
72 <param name="source" value="history" />
73 <param name="input_bed" value="zika/db/zika_primers.bed" />
74 </conditional>
48 <param name="input_bam" value="zika/Z52_b.sorted.bam" /> 75 <param name="input_bam" value="zika/Z52_b.sorted.bam" />
49 <param name="input_bed" value="zika/db/zika_primers.bed" />
50 <output name="output_bam" file="zika/Z52_b.trimmed.sorted.bam" compare="sim_size" delta="100000"/> 76 <output name="output_bam" file="zika/Z52_b.trimmed.sorted.bam" compare="sim_size" delta="100000"/>
77 </test>
78 <test>
79 <conditional name="primer">
80 <param name="source" value="cached" />
81 <param name="cached_bed" value="SARS-CoV-2-ARTICv1" />
82 </conditional>
83 <param name="input_bam" value="sars-cov-2/sars_cov2_untrimmed.bam" ftype="bam" />
84 <output name="output_bam" file="sars-cov-2/sars_cov2_trimmed.bam" />
51 </test> 85 </test>
52 </tests> 86 </tests>
53 <help><![CDATA[ 87 <help><![CDATA[
54 iVar uses primer positions supplied in a BED file to soft clip primer 88 iVar uses primer positions supplied in a BED file to soft clip primer
55 sequences from an aligned and sorted BAM file. Following this, the reads are 89 sequences from an aligned and sorted BAM file. Following this, the reads are