Mercurial > repos > iuc > trinity
diff trinity.xml @ 20:171b827eadf2 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
| author | iuc |
|---|---|
| date | Thu, 14 Jun 2018 03:11:11 -0400 |
| parents | cee61b3fcf78 |
| children | c9cfec002f71 |
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--- a/trinity.xml Mon Jan 22 11:26:29 2018 -0500 +++ b/trinity.xml Thu Jun 14 03:11:11 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="trinity" name="Trinity" version="@WRAPPER_VERSION@.2"> +<tool id="trinity" name="Trinity" version="@WRAPPER_VERSION@"> <description>de novo assembly of RNA-Seq data</description> <macros> <import>macros.xml</import> @@ -22,48 +22,66 @@ #end if Trinity --no_version_check - ## Inputs. - #if $inputs.paired_or_single == "paired": - - --left ${ ','.join(['"%s"' % x for x in $inputs.left_input]) } - - --right ${ ','.join(['"%s"' % x for x in $inputs.right_input]) } + ## Inputs + #if $pool.pool_mode == "Yes": + #if str($pool.inputs.paired_or_single) == "single": + --single ${ ','.join(['"%s"' % x for x in $pool.inputs.input]) } + #if $pool.inputs.input[0].is_of_type('fasta'): + --seqType fa + #else: + --seqType fq + #end if - #if $inputs.left_input[0].is_of_type('fasta'): - --seqType fa - #else: - --seqType fq - #end if + #if $pool.inputs.strand.is_strand_specific: + --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]) } - @COMMAND_PAIRED_STRAND_JACCARD@ - - #elif $inputs.paired_or_single == "paired_collection" - --left ${ ','.join(['"%s"' % x.forward for x in $inputs.pair_input]) } - - --right ${ ','.join(['"%s"' % x.reverse for x in $inputs.pair_input]) } + --right ${ ','.join(['"%s"' % x for x in $pool.inputs.right_input]) } - #if $inputs.pair_input[0].forward.is_of_type('fasta'): - --seqType fa - #else: - --seqType fq + #if $pool.inputs.left_input[0].is_of_type('fasta'): + --seqType fa + #else: + --seqType fq + #end if + @COMMAND_PAIRED_STRAND_JACCARD@ + #elif str($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]) } + #if $pool.inputs.pair_input[0].forward.is_of_type('fasta'): + --seqType fa + #else: + --seqType fq + #end if + @COMMAND_PAIRED_STRAND_JACCARD@ #end if - - @COMMAND_PAIRED_STRAND_JACCARD@ + #elif $pool.pool_mode == "No": + #if $pool.inputs.paired_or_single == "unmerged_paired_collection": + --left $pool.inputs.pair_input.forward - #else: - --single ${ ','.join(['"%s"' % x for x in $inputs.input]) } + --right $pool.inputs.pair_input.reverse - #if $inputs.input[0].is_of_type('fasta'): - --seqType fa - #else: - --seqType fq - #end if + #if $pool.inputs.pair_input.forward.is_of_type('fasta'): + --seqType fa + #else: + --seqType fq + #end if + @COMMAND_PAIRED_STRAND_JACCARD@ + #elif $pool.inputs.paired_or_single == "unmerged_single_collection": + --single $pool.inputs.input - #if $inputs.strand.is_strand_specific: - --SS_lib_type $inputs.strand.library_type + #if $pool.inputs.input.is_of_type('fasta'): + --seqType fa + #else: + --seqType fq + #end if + + #if $pool.inputs.strand.is_strand_specific: + --SS_lib_type $pool.inputs.strand.library_type + #end if #end if #end if - $norm ## Additional parameters. @@ -87,7 +105,6 @@ #if $additional_params.guided.genome_guided_max_intron: --genome_guided_max_intron $additional_params.guided.genome_guided_max_intron #end if - #end if #if $additional_params.min_kmer_cov: @@ -109,39 +126,71 @@ ]]></command> <inputs> - <conditional name="inputs"> - <param name="paired_or_single" type="select" label="Paired or Single-end data?"> - <option value="single">Single-end</option> - <option value="paired" selected="true">Paired-end</option> - <option value="paired_collection">Paired-end collection</option> + <conditional name="pool"> + <param name="pool_mode" type="select" label="Are you pooling sequence datasets?" help="" > + <option value="No">No</option> + <option value="Yes" selected="True">Yes</option> </param> - <when value="single"> - <param name="input" argument="--single" type="data" format="fasta,fastqsanger" multiple="true" label="Single-end reads" help=""/> - <conditional name="strand"> - <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/> - <when value="false"> + <when value="Yes" > + <conditional name="inputs"> + <param name="paired_or_single" type="select" label="Paired or Single-end data?"> + <option value="single" selected="true">Single-end</option> + <option value="paired">Paired-end</option> + <option value="paired_collection">Paired-end collection</option> + </param> + <when value="single"> + <param name="input" argument="--single" type="data" format="fasta,fastqsanger" multiple="true" label="Single-end reads" help=""/> + <conditional name="strand"> + <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/> + <when value="false"> + </when> + <when value="true"> + <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific Library Type"> + <option value="F">F</option> + <option value="R">R</option> + </param> + </when> + </conditional> </when> - <when value="true"> - <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific Library Type"> - <option value="F">F</option> - <option value="R">R</option> - </param> + <when value="paired"> + <param name="left_input" argument="--left" type="data" format="fasta,fastqsanger" multiple="true" label="Left/Forward strand reads" /> + <param name="right_input" argument="--right" type="data" format="fasta,fastqsanger" multiple="true" label="Right/Reverse strand reads" /> + <expand macro="input_paired_strand_jaccard" /> + </when> + <when value="paired_collection"> + <param name="pair_input" type="data_collection" collection_type="list:paired" format="fasta,fastqsanger" label="FASTA/FASTQ dataset collection with R1/R2 pair" help="Can be lists of pair dataset collection"/> + <expand macro="input_paired_strand_jaccard" /> </when> </conditional> </when> - <when value="paired"> - <param name="left_input" argument="--left" type="data" format="fasta,fastqsanger" multiple="true" label="Left/Forward strand reads" /> - <param name="right_input" argument="--right" type="data" format="fasta,fastqsanger" multiple="true" label="Right/Reverse strand reads" /> - <expand macro="input_paired_strand_jaccard" /> - </when> - <when value="paired_collection"> - <param name="pair_input" type="data_collection" collection_type="list:paired" format="fasta,fastqsanger" label="FASTA/FASTQ dataset collection with R1/R2 pair" help="Can be lists of pair dataset collection"/> - <expand macro="input_paired_strand_jaccard" /> + <when value="No"> + <conditional name="inputs"> + <param name="paired_or_single" type="select" label="Paired or Single-end data?"> + <option value="unmerged_single_collection">Single-end</option> + <option value="unmerged_paired_collection">Paired-end</option> + </param> + <when value="unmerged_single_collection"> + <param name="input" argument="--single" type="data" format="fasta,fastqsanger" label="Single-end reads" help="Elements of collection will NOT be merged"/> + <conditional name="strand"> + <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/> + <when value="false"> + </when> + <when value="true"> + <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific Library Type"> + <option value="F">F</option> + <option value="R">R</option> + </param> + </when> + </conditional> + </when> + <when value="unmerged_paired_collection"> + <param name="pair_input" type="data_collection" collection_type="paired" format="fasta,fastqsanger" label="FASTA/FASTQ dataset collection with R1/R2 pair" help="Pair dataset collection. The paired datasets will NOT be merged"/> + <expand macro="input_paired_strand_jaccard" /> + </when> + </conditional> </when> </conditional> - <param name="norm" type="boolean" argument="--normalize_reads" truevalue="--normalize_reads" falsevalue="" checked="true" label="Run in silico normalization of reads" help="Defaults to max. read coverage of 50."/> - <section name="additional_params" title="Additional Options" expanded="False"> <param name="min_contig_length" argument="--min_contig_length" type="integer" optional="true" value="200" min="1" label="Minimum Contig Length" help="All contigs shorter than this will be discarded"/> @@ -167,9 +216,36 @@ </inputs> <outputs> <data name="assembled_transcripts" format="fasta" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir/Trinity.fasta"/> + <data name="gene_to_trans" format="tabular" label="${tool.name} on ${on_string}: Gene to transcripts map" from_work_dir="trinity_out_dir/Trinity.fasta.gene_trans_map"/> </outputs> <tests> <test> + <param name="pool_mode" value="No" /> + <param name="paired_or_single" value="unmerged_paired_collection"/> + <param name="pair_input"> + <collection type="paired"> + <element name="forward" value="reads.left.fq" ftype="fastqsanger" /> + <element name="reverse" value="reads.right.fq" ftype="fastqsanger"/> + </collection> + </param> + <param name="is_strand_specific" value="true"/> + <param name="norm" value="true"/> + <param name="library_type" value="RF"/> + <output name="assembled_transcripts" file="norm/Trinity_paired_unmerged_1.fasta" compare="sim_size" delta="500" /> + <output name="gene_to_trans" file="norm/Trinity_paired_unmerged_1.map" compare="sim_size" /> + </test> + <test> + <param name="pool_mode" value="No" /> + <param name="paired_or_single" value="unmerged_single_collection"/> + <param name="input" value="reads.left.fq" ftype="fastqsanger"/> + <param name="is_strand_specific" value="true"/> + <param name="norm" value="false"/> + <param name="library_type" value="F"/> + <output name="assembled_transcripts" file="raw/Trinity_single_unmerged_1.fasta" compare="sim_size" delta="500" /> + <output name="gene_to_trans" file="raw/Trinity_single_unmerged_1.map" compare="sim_size" /> + </test> + <test> + <param name="pool_mode" value="Yes" /> <param name="paired_or_single" value="paired"/> <param name="left_input" value="reads.left.fq" ftype="fastqsanger"/> <param name="right_input" value="reads.right.fq" ftype="fastqsanger"/> @@ -177,8 +253,10 @@ <param name="norm" value="false"/> <param name="library_type" value="RF"/> <output name="assembled_transcripts" file="raw/Trinity.fasta" compare="sim_size" delta="500" /> + <output name="gene_to_trans" file="raw/Trinity.map" compare="sim_size" /> </test> <test> + <param name="pool_mode" value="Yes" /> <param name="paired_or_single" value="paired"/> <param name="left_input" value="reads.left.fq" ftype="fastqsanger"/> <param name="right_input" value="reads.right.fq" ftype="fastqsanger"/> @@ -186,8 +264,10 @@ <param name="norm" value="true"/> <param name="library_type" value="RF"/> <output name="assembled_transcripts" file="norm/Trinity.fasta" compare="sim_size" delta="500" /> + <output name="gene_to_trans" file="norm/Trinity.map" compare="sim_size" /> </test> <test> + <param name="pool_mode" value="Yes" /> <param name="paired_or_single" value="paired_collection"/> <param name="pair_input"> <collection type="list:paired"> @@ -209,6 +289,7 @@ <param name="norm" value="true"/> <param name="library_type" value="RF"/> <output name="assembled_transcripts" file="norm/Trinity.fasta" compare="sim_size" delta="500" /> + <output name="gene_to_trans" file="norm/Trinity.map" compare="sim_size" /> </test> </tests> <help> @@ -216,6 +297,5 @@ .. _Trinity: http://trinityrnaseq.github.io </help> - <expand macro="citation" /> </tool>