Mercurial > repos > iuc > coverm_genome
changeset 4:c4e3aa19841c draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit bc3831e3648809bd3d46611b2a74bd26a17985e5
| author | iuc |
|---|---|
| date | Fri, 18 Aug 2023 09:22:54 +0000 |
| parents | dd96e74908a9 |
| children | |
| files | macros.xml |
| diffstat | 1 files changed, 5 insertions(+), 8 deletions(-) [+] |
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--- a/macros.xml Wed Jul 26 07:34:11 2023 +0000 +++ b/macros.xml Fri Aug 18 09:22:54 2023 +0000 @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">0.6.1</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@VERSION_SUFFIX@">2</token> <token name="@PROFILE@">22.01</token> <xml name="requirements"> <requirements> @@ -118,9 +118,6 @@ <option value="interleaved">Interleaved</option> </param> </xml> - <xml name="paired_reads"> - <param name="paired_reads" type="data_collection" collection_type="list:paired" format="@INPUT_FORMATS@" label="Collection of paired-end FASTA/Q files(s) for mapping" help="One or more pairs of forward and reverse possibly gzipped FASTA/Q files for mapping in order." /> - </xml> <xml name="individual_assembly_reads"> <conditional name="read_type"> <expand macro="read_type"/> @@ -132,7 +129,7 @@ <param argument="-2" name="read2" type="data" format="@INPUT_FORMATS@" label="Reverse FASTA/Q file for mapping" /> </when> <when value="paired_collection"> - <expand macro="paired_reads"/> + <param name="paired_reads" type="data_collection" collection_type="paired" format="@INPUT_FORMATS@" label="Collection of paired-end FASTA/Q files(s) for mapping" help="One or more pairs of forward and reverse possibly gzipped FASTA/Q files for mapping in order." /> </when> <when value="interleaved"> <param argument="--interleaved" type="data" format="@INPUT_FORMATS@" label="Interleaved FASTA/Q files for mapping" /> @@ -168,7 +165,7 @@ ln -s '$reads.paired_reads.forward' '$fn' && #set $fn = "rv/" + $id #silent $rv_fp.append( $fn ) -ln -s '$mreads.paired_reads.reverse' '${fn}' && +ln -s '$reads.paired_reads.reverse' '$fn' && #else if $reads.type == 'interleaved' #set $fn = "interl/" + re.sub('[^\s\w\-\\.]', '_', str($reads.interleaved.element_identifier)) #silent $interl_fp.append( $fn ) @@ -206,7 +203,7 @@ <param argument="-2" name="read2" type="data" format="@INPUT_FORMATS@" multiple="true" label="Reverse FASTA/Q file(s) for mapping" /> </when> <when value="paired_collection"> - <expand macro="paired_reads"/> + <param name="paired_reads" type="data_collection" collection_type="list:paired" format="@INPUT_FORMATS@" label="Collection of paired-end FASTA/Q files(s) for mapping" help="One or more pairs of forward and reverse possibly gzipped FASTA/Q files for mapping in order." /> </when> <when value="interleaved"> <param argument="--interleaved" type="data" format="@INPUT_FORMATS@" multiple="true" label="Interleaved FASTA/Q files(s) for mapping" /> @@ -341,4 +338,4 @@ <yield /> </citations> </xml> -</macros> \ No newline at end of file +</macros>