Mercurial > repos > iuc > concoct_coverage_table
changeset 3:5ded3318cf8a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/concoct commit 58c54ba18f478ce75fdfd6093921ba0b50af02ac
| author | iuc |
|---|---|
| date | Wed, 03 Aug 2022 13:56:39 +0000 |
| parents | 6302656ed45d |
| children | 0442e7102125 |
| files | concoct_coverage_table.xml macros.xml test-data/ten_reads_two_contigs-s_2.bam |
| diffstat | 3 files changed, 48 insertions(+), 12 deletions(-) [+] |
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--- a/concoct_coverage_table.xml Thu Jul 07 08:32:46 2022 +0000 +++ b/concoct_coverage_table.xml Wed Aug 03 13:56:39 2022 +0000 @@ -3,24 +3,42 @@ <macros> <import>macros.xml</import> </macros> - <expand macro="requirements"> - <requirement type="package" version="1.15.1">samtools</requirement> - </expand> + <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ +#import re mkdir 'mapping' && -#for $e in $bamfiles - ln -s '$e' 'mapping/${e.element_identifier}.sorted.bam' && - samtools index 'mapping/${e.element_identifier}.sorted.bam' 'mapping/${e.element_identifier}.bam.bai' && - mv 'mapping/${e.element_identifier}.sorted.bam' 'mapping/${e.element_identifier}.bam' && -#end for +#if $mode.type == 'individual' + #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($mode.bamfile)) +ln -s '$mode.bamfile' 'mapping/${identifier}.sorted.bam' && +samtools index 'mapping/${identifier}.sorted.bam' 'mapping/${identifier}.bam.bai' && +mv 'mapping/${identifier}.sorted.bam' 'mapping/${identifier}.bam' && +#else + #for $e in $mode.bamfiles + #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($e.element_identifier)) +ln -s '$e' 'mapping/${identifier}.sorted.bam' && +samtools index 'mapping/${identifier}.sorted.bam' 'mapping/${identifier}.bam.bai' && +mv 'mapping/${identifier}.sorted.bam' 'mapping/${identifier}.bam' && + #end for +#end if concoct_coverage_table.py '$bedfile' mapping/*.bam > '$output' ]]></command> <inputs> - <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."/> - <param name="bamfiles" type="data" format="bam" label="Sorted BAM files" multiple="true" help="BAM files with mappings to the original contigs, after sorting"/> + <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."/> + <conditional name="mode"> + <param name="type" type="select" label="Type of assembly used to generate the contigs" help="Information used to process the BAM files"> + <option value="individual">Individual assembly: 1 run per BAM file</option> + <option value="co">Co-assembly: all BAM files processed together</option> + </param> + <when value="individual"> + <param name="bamfile" type="data" format="bam" label="Sorted BAM file" help="BAM file with mappings to the original contigs, after sorting"/> + </when> + <when value="co"> + <param name="bamfiles" type="data" format="bam" label="Sorted BAM files" multiple="true" help="BAM files with mappings to the original contigs, after sorting"/> + </when> + </conditional> </inputs> <outputs> <data name="output" format="tabular"/> @@ -28,7 +46,10 @@ <tests> <test expect_num_outputs="1"> <param name="bedfile" value="two_contigs-cut2.bed" ftype="bed"/> - <param name="bamfiles" value="ten_reads_two_contigs-s.bam" ftype="bam"/> + <conditional name="mode"> + <param name="type" value="individual"/> + <param name="bamfile" value="ten_reads_two_contigs-s.bam" ftype="bam"/> + </conditional> <output name="output" ftype="tabular"> <assert_contents> <has_text text="contig-21000001.concoct_part_0"/> @@ -36,6 +57,21 @@ </assert_contents> </output> </test> + <test expect_num_outputs="1"> + <param name="bedfile" value="two_contigs-cut2.bed" ftype="bed"/> + <conditional name="mode"> + <param name="type" value="co"/> + <param name="bamfiles" value="ten_reads_two_contigs-s.bam,ten_reads_two_contigs-s_2.bam" ftype="bam"/> + </conditional> + <output name="output" ftype="tabular"> + <assert_contents> + <has_text text="cov_mean_sample_ten_reads_two_contigs-s.bam"/> + <has_text text="cov_mean_sample_ten_reads_two_contigs-s_2.bam"/> + <has_text text="contig-21000001.concoct_part_0"/> + <has_n_lines n="11"/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[ **What it does**
--- a/macros.xml Thu Jul 07 08:32:46 2022 +0000 +++ b/macros.xml Wed Aug 03 13:56:39 2022 +0000 @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">1.1.0</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <token name="@PROFILE@">21.01</token> <xml name="requirements"> <requirements>