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comparison concoct_coverage_table.xml @ 3:9e924fbcbcee draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 58c54ba18f478ce75fdfd6093921ba0b50af02ac
author iuc
date Wed, 03 Aug 2022 13:53:23 +0000
parents 2b6ed3a91fbe
children
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2:2b6ed3a91fbe 3:9e924fbcbcee
1 <tool id="concoct_coverage_table" name="CONCOCT: Generate the input coverage table" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> 1 <tool id="concoct_coverage_table" name="CONCOCT: Generate the input coverage table" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>for CONCOCT</description> 2 <description>for CONCOCT</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" version="1.15.1">samtools</requirement>
8 </expand>
9 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 #import re
10 mkdir 'mapping' && 9 mkdir 'mapping' &&
11 #for $e in $bamfiles 10 #if $mode.type == 'individual'
12 ln -s '$e' 'mapping/${e.element_identifier}.sorted.bam' && 11 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($mode.bamfile))
13 samtools index 'mapping/${e.element_identifier}.sorted.bam' 'mapping/${e.element_identifier}.bam.bai' && 12 ln -s '$mode.bamfile' 'mapping/${identifier}.sorted.bam' &&
14 mv 'mapping/${e.element_identifier}.sorted.bam' 'mapping/${e.element_identifier}.bam' && 13 samtools index 'mapping/${identifier}.sorted.bam' 'mapping/${identifier}.bam.bai' &&
15 #end for 14 mv 'mapping/${identifier}.sorted.bam' 'mapping/${identifier}.bam' &&
15 #else
16 #for $e in $mode.bamfiles
17 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($e.element_identifier))
18 ln -s '$e' 'mapping/${identifier}.sorted.bam' &&
19 samtools index 'mapping/${identifier}.sorted.bam' 'mapping/${identifier}.bam.bai' &&
20 mv 'mapping/${identifier}.sorted.bam' 'mapping/${identifier}.bam' &&
21 #end for
22 #end if
16 concoct_coverage_table.py 23 concoct_coverage_table.py
17 '$bedfile' 24 '$bedfile'
18 mapping/*.bam 25 mapping/*.bam
19 > '$output' 26 > '$output'
20 ]]></command> 27 ]]></command>
21 <inputs> 28 <inputs>
22 <param name="bedfile" type="data" format="bed" label="Contigs BEDFile" help="The file should have four columns representing: 'Contig ID, Start Position, End Position and SubContig ID' respectively. The Subcontig ID must contain the pattern 'concoct_part_[0-9]*' while the contigs which are not cutup cannot contain this pattern. This file can be generated by the cut_up_fasta tool."/> 29 <param name="bedfile" type="data" format="bed" label="Contigs BEDFile" help="The file should have four columns representing: 'Contig ID, Start Position, End Position and SubContig ID' respectively. The Subcontig ID must contain the pattern 'concoct_part_[0-9]*' while the contigs which are not cutup cannot contain this pattern. This file can be generated by the CONCOCT: Cut up contigs tool."/>
23 <param name="bamfiles" type="data" format="bam" label="Sorted BAM files" multiple="true" help="BAM files with mappings to the original contigs, after sorting"/> 30 <conditional name="mode">
31 <param name="type" type="select" label="Type of assembly used to generate the contigs" help="Information used to process the BAM files">
32 <option value="individual">Individual assembly: 1 run per BAM file</option>
33 <option value="co">Co-assembly: all BAM files processed together</option>
34 </param>
35 <when value="individual">
36 <param name="bamfile" type="data" format="bam" label="Sorted BAM file" help="BAM file with mappings to the original contigs, after sorting"/>
37 </when>
38 <when value="co">
39 <param name="bamfiles" type="data" format="bam" label="Sorted BAM files" multiple="true" help="BAM files with mappings to the original contigs, after sorting"/>
40 </when>
41 </conditional>
24 </inputs> 42 </inputs>
25 <outputs> 43 <outputs>
26 <data name="output" format="tabular"/> 44 <data name="output" format="tabular"/>
27 </outputs> 45 </outputs>
28 <tests> 46 <tests>
29 <test expect_num_outputs="1"> 47 <test expect_num_outputs="1">
30 <param name="bedfile" value="two_contigs-cut2.bed" ftype="bed"/> 48 <param name="bedfile" value="two_contigs-cut2.bed" ftype="bed"/>
31 <param name="bamfiles" value="ten_reads_two_contigs-s.bam" ftype="bam"/> 49 <conditional name="mode">
50 <param name="type" value="individual"/>
51 <param name="bamfile" value="ten_reads_two_contigs-s.bam" ftype="bam"/>
52 </conditional>
32 <output name="output" ftype="tabular"> 53 <output name="output" ftype="tabular">
33 <assert_contents> 54 <assert_contents>
55 <has_text text="contig-21000001.concoct_part_0"/>
56 <has_n_lines n="11"/>
57 </assert_contents>
58 </output>
59 </test>
60 <test expect_num_outputs="1">
61 <param name="bedfile" value="two_contigs-cut2.bed" ftype="bed"/>
62 <conditional name="mode">
63 <param name="type" value="co"/>
64 <param name="bamfiles" value="ten_reads_two_contigs-s.bam,ten_reads_two_contigs-s_2.bam" ftype="bam"/>
65 </conditional>
66 <output name="output" ftype="tabular">
67 <assert_contents>
68 <has_text text="cov_mean_sample_ten_reads_two_contigs-s.bam"/>
69 <has_text text="cov_mean_sample_ten_reads_two_contigs-s_2.bam"/>
34 <has_text text="contig-21000001.concoct_part_0"/> 70 <has_text text="contig-21000001.concoct_part_0"/>
35 <has_n_lines n="11"/> 71 <has_n_lines n="11"/>
36 </assert_contents> 72 </assert_contents>
37 </output> 73 </output>
38 </test> 74 </test>