Mercurial > repos > iuc > trinity
changeset 27:5b60313a6ce7 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e8eb8467278032fd21f513fddf0b082b22aee42d"
| author | iuc |
|---|---|
| date | Wed, 12 May 2021 08:54:43 +0000 |
| parents | 26d5493b20b6 |
| children | 48636f857c4b |
| files | trinity.xml |
| diffstat | 1 files changed, 38 insertions(+), 11 deletions(-) [+] |
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--- a/trinity.xml Fri Mar 19 21:43:30 2021 +0000 +++ b/trinity.xml Wed May 12 08:54:43 2021 +0000 @@ -20,12 +20,39 @@ ln -s '${$additional_params.guided.genome_guided_bam}' 'localbam.bam' && ln -s '${$additional_params.guided.genome_guided_bam.metadata.bam_index}' 'localbam.bam.bai' && #end if + #if $pool.pool_mode == "Yes": + #if str($pool.inputs.paired_or_single) == "single": + #for i, f in enumerate($pool.inputs.input): + ln -s '$f' input${i}.${f.ext} && + #end for + #elif str($pool.inputs.paired_or_single) == "paired": + #for i, f in enumerate($pool.inputs.left_input): + ln -s '$f' left_input${i}.${f.ext} && + #end for + #for i, f in enumerate($pool.inputs.right_input): + ln -s '$f' right_input${i}.${f.ext} && + #end for + #elif str($pool.inputs.paired_or_single) == "paired_collection": + #for i, f in enumerate($pool.inputs.pair_input): + ln -s '$f.forward' 'left_input${i}.${f.forward.ext}' && + ln -s '$f.reverse' 'right_input${i}.${f.reverse.ext}' && + #end for + #end if + #elif $pool.pool_mode == "No": + #if $pool.inputs.paired_or_single == "unmerged_paired_collection": + ln -s '$pool.inputs.pair_input.forward' 'left_input.${$pool.inputs.pair_input.forward.ext}' && + ln -s '$pool.inputs.pair_input.reverse' 'right_input.${pool.inputs.pair_input.reverse.ext}' && + #elif $pool.inputs.paired_or_single == "unmerged_single_collection": + ln -s '$pool.inputs.input' 'input.${pool.inputs.input.ext}' && + #end if + #end if + Trinity --no_version_check ## Inputs #if $pool.pool_mode == "Yes": #if str($pool.inputs.paired_or_single) == "single": - --single ${ ','.join(['"%s"' % x for x in $pool.inputs.input]) } + --single ${ ','.join(["'input%s.%s'" % ($i, $f.ext) for i, f in enumerate($pool.inputs.input)]) } #if $pool.inputs.input[0].is_of_type('fasta'): --seqType fa #else: @@ -36,9 +63,9 @@ --SS_lib_type $pool.inputs.strand.library_type #end if #elif str($pool.inputs.paired_or_single) == "paired": - --left ${ ','.join(['"%s"' % x for x in $pool.inputs.left_input]) } + --left ${ ','.join(["'left_input%s.%s'" % ($i, $f.ext) for i, f in enumerate($pool.inputs.left_input)]) } - --right ${ ','.join(['"%s"' % x for x in $pool.inputs.right_input]) } + --right ${ ','.join(["'right_input%s.%s'" % ($i, $f.ext) for i, f in enumerate($pool.inputs.right_input)]) } #if $pool.inputs.left_input[0].is_of_type('fasta'): --seqType fa @@ -47,8 +74,8 @@ #end if @COMMAND_PAIRED_STRAND_JACCARD@ #elif str($pool.inputs.paired_or_single) == "paired_collection": - --left ${ ','.join(['"%s"' % x.forward for x in $pool.inputs.pair_input]) } - --right ${ ','.join(['"%s"' % x.reverse for x in $pool.inputs.pair_input]) } + --left ${ ','.join(["'left_input%s.%s'" % ($i, $f.forward.ext) for i, f in enumerate($pool.inputs.pair_input)]) } + --right ${ ','.join(["'right_input%s.%s'" % ($i, $f.reverse.ext) for i, f in enumerate($pool.inputs.pair_input)]) } #if $pool.inputs.pair_input[0].forward.is_of_type('fasta'): --seqType fa #else: @@ -58,9 +85,9 @@ #end if #elif $pool.pool_mode == "No": #if $pool.inputs.paired_or_single == "unmerged_paired_collection": - --left $pool.inputs.pair_input.forward + --left 'left_input.${$pool.inputs.pair_input.forward.ext}' - --right $pool.inputs.pair_input.reverse + --right 'right_input.${pool.inputs.pair_input.reverse.ext}' #if $pool.inputs.pair_input.forward.is_of_type('fasta'): --seqType fa @@ -69,9 +96,9 @@ #end if @COMMAND_PAIRED_STRAND_JACCARD@ #elif $pool.inputs.paired_or_single == "unmerged_single_collection": - --single $pool.inputs.input + --single 'input.${pool.inputs.input.ext}' - #if $pool.inputs.input.is_of_type('fasta'): + #if $pool.inputs.input.is_of_type('fasta'): --seqType fa #else: --seqType fq @@ -239,8 +266,8 @@ <param name="paired_or_single" value="unmerged_paired_collection"/> <param name="pair_input"> <collection type="paired"> - <element name="forward" value="reads.left.fq.gz" ftype="fastqsanger" /> - <element name="reverse" value="reads.right.fq.gz" ftype="fastqsanger"/> + <element name="forward" value="reads.left.fq.gz" ftype="fastqsanger.gz" /> + <element name="reverse" value="reads.right.fq.gz" ftype="fastqsanger.gz" /> </collection> </param> <param name="is_strand_specific" value="true"/>