| Previous changeset 2:de0af39266ef (2016-04-25) Next changeset 4:692491de7df5 (2016-05-12) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bbfd77c34b609b86ef3a24525dae1127d8b3d99b |
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modified:
abundance_estimates_to_matrix.xml align_and_estimate_abundance.xml run_DE_analysis.xml tool_dependencies.xml trinity.xml |
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| diff -r de0af39266ef -r c7555bc21812 abundance_estimates_to_matrix.xml --- a/abundance_estimates_to_matrix.xml Mon Apr 25 10:02:37 2016 -0400 +++ b/abundance_estimates_to_matrix.xml Tue May 03 10:54:25 2016 -0400 |
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| @@ -26,13 +26,13 @@ #end for ]]></command> <inputs> - <repeat name="samples" title="RSEM abundance estimates for samples"> + <repeat name="samples" title="Abundance estimates for samples"> <param name="file" label="Add file" type="data" format="tabular"/> <param name="sample_name" label="Sample name" type="text"> <validator type="regex" message="Value must be a not empty string composed by alphanumeric characters and underscores">^\w+$</validator> </param> </repeat> - + <param type="select" name="est_method" label="Abundance estimation method"> <option value="RSEM">RSEM</option> <option value="eXpress">eXpress</option> @@ -198,7 +198,7 @@ .. _Trinity: http://trinityrnaseq.github.io ]]> </help> - + <citations> <citation type="doi">doi:10.1038/nbt.1883</citation> </citations> |
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| diff -r de0af39266ef -r c7555bc21812 align_and_estimate_abundance.xml --- a/align_and_estimate_abundance.xml Mon Apr 25 10:02:37 2016 -0400 +++ b/align_and_estimate_abundance.xml Tue May 03 10:54:25 2016 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="align_and_estimate_abundance" name="Align reads and estimate abundance" version="2.1.1"> +<tool id="align_and_estimate_abundance" name="Align reads and estimate abundance" version="2.1.1.1"> <description>on a de novo assembly of RNA-Seq data</description> <requirements> <requirement type="package" version="2.1.1">trinity</requirement> @@ -17,7 +17,7 @@ && align_and_estimate_abundance.pl - + --transcripts input.fa --est_method $method.est_method @@ -27,42 +27,42 @@ #if $inputs.paired_or_single == "paired": --left $inputs.left_input --right $inputs.right_input - + #if $inputs.left_input.is_of_type('fasta'): --seqType fa #else: --seqType fq #end if - + #if $inputs.strand.is_strand_specific: --SS_lib_type $inputs.strand.library_type #end if #else: --single $inputs.input - + #if $inputs.input.is_of_type('fasta'): --seqType fa #else: --seqType fq #end if - + #if $inputs.strand.is_strand_specific: --SS_lib_type $inputs.strand.library_type #end if #end if - + --max_ins_size $inputs.paired_fragment_length ## Additional parameters. - #if $additional_params.gene_map.has_gene_map == "yes": + #if $additional_params.gene_map.has_gene_map == "no": --gene_trans_map $additional_params.gene_map.gene_trans_map #else --trinity_mode #end if - + --prep_reference - + --output_dir . ## CPU @@ -106,7 +106,7 @@ </conditional> </when> </conditional> - + <conditional name="method"> <param type="select" name="est_method" label="Abundance estimation method"> <option value="RSEM">RSEM</option> @@ -129,16 +129,16 @@ <section name="additional_params" title="Additional Options" expanded="False"> <conditional name="gene_map"> <param name="has_gene_map" type="select" label="Trinity assembly?" help="If the transcripts were not assembled by trinity, additional information is needed"> + <option value="yes">Yes</option> <option value="no">No</option> - <option value="yes">Yes</option> </param> - <when value="no"> + <when value="yes"> </when> - <when value="yes"> + <when value="no"> <param format="tabular" name="gene_trans_map" type="data" label="Gene to transcript correspondence ('gene(tab)transcript' lines)" /> </when> </conditional> - + </section> </inputs> <outputs> @@ -148,7 +148,7 @@ <data format="tabular" name="genes_counts_rsem" label="${tool.name} on ${on_string}: genes counts" from_work_dir="RSEM.genes.results"> <filter>method['est_method'] == "RSEM"</filter> </data> - + <data format="tabular" name="isoforms_counts_express" label="${tool.name} on ${on_string}: isoforms counts" from_work_dir="results.xprs"> <filter>method['est_method'] == "eXpress"</filter> </data> @@ -165,7 +165,7 @@ <param name="library_type" value="RF"/> <param name="est_method" value="RSEM"/> <param name="aln_method" value="bowtie"/> - <param name="has_gene_map" value="no"/> + <param name="has_gene_map" value="yes"/> <output name="isoforms_counts_rsem"> <assert_contents> <has_line_matching expression="TRINITY_DN0_c0_g1_i1	.*" /> @@ -187,7 +187,7 @@ <param name="library_type" value="RF"/> <param name="est_method" value="RSEM"/> <param name="aln_method" value="bowtie2"/> - <param name="has_gene_map" value="no"/> + <param name="has_gene_map" value="yes"/> <output name="isoforms_counts_rsem"> <assert_contents> <has_line_matching expression="TRINITY_DN0_c0_g1_i1	.*" /> @@ -209,7 +209,7 @@ <param name="library_type" value="RF"/> <param name="est_method" value="eXpress"/> <param name="aln_method" value="bowtie"/> - <param name="has_gene_map" value="no"/> + <param name="has_gene_map" value="yes"/> <output name="isoforms_counts_express"> <assert_contents> <has_line_matching expression=".*	TRINITY_DN2_c3_g1_i1	.*" /> @@ -252,7 +252,7 @@ .. _Trinity: http://trinityrnaseq.github.io ]]> </help> - + <citations> <citation type="doi">doi:10.1038/nbt.1883</citation> </citations> |
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| diff -r de0af39266ef -r c7555bc21812 run_DE_analysis.xml --- a/run_DE_analysis.xml Mon Apr 25 10:02:37 2016 -0400 +++ b/run_DE_analysis.xml Tue May 03 10:54:25 2016 -0400 |
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| @@ -7,7 +7,7 @@ <requirement type="package" version="1.10.0">bioconductor-deseq2</requirement> <requirement type="package" version="3.12.0">edger</requirement> <requirement type="package" version="3.12.0">bioconductor-edger</requirement> - <requirement type="package" version="3.25.3">limma</requirement> + <requirement type="package" version="3.27.4">limma</requirement> <requirement type="package" version="3.27.4">bioconductor-limma</requirement> </requirements> <stdio> |
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| diff -r de0af39266ef -r c7555bc21812 tool_dependencies.xml --- a/tool_dependencies.xml Mon Apr 25 10:02:37 2016 -0400 +++ b/tool_dependencies.xml Tue May 03 10:54:25 2016 -0400 |
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| @@ -1,7 +1,7 @@ <?xml version="1.0"?> <tool_dependency> <package name="trinity" version="2.1.1"> - <repository changeset_revision="b66b28a11557" name="package_trinity_2_1_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="f75117647d9c" name="package_trinity_2_1_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="bowtie" version="1.1.2"> <repository changeset_revision="a1c1a92e13a6" name="package_bowtie_1_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> @@ -25,7 +25,7 @@ <repository changeset_revision="7c305aa20292" name="package_r_limma_3_27_4" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="deseq2" version="1.10.0"> - <repository changeset_revision="362a2224b1d2" name="package_deseq2_1_10_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="56a98b4043fd" name="package_deseq2_1_10_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <set_environment version="1.0"> <environment_variable action="set_to" name="TRINITY_MEM_OPTIONS">--max_memory 30G --bflyHeapSpaceMax 30G</environment_variable> |
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| diff -r de0af39266ef -r c7555bc21812 trinity.xml --- a/trinity.xml Mon Apr 25 10:02:37 2016 -0400 +++ b/trinity.xml Tue May 03 10:54:25 2016 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="trinity" name="Trinity" version="2.1.1"> +<tool id="trinity" name="Trinity" version="2.1.1.1"> <description>de novo assembly of RNA-Seq data</description> <requirements> <requirement type="package" version="2.1.1">trinity</requirement> @@ -11,34 +11,37 @@ ## Inputs. #if $inputs.paired_or_single == "paired": - --left $inputs.left_input --right $inputs.right_input - - #if $inputs.left_input.is_of_type('fasta'): + + --left ${ ','.join(['"%s"' % x for x in $inputs.left_input]) } + + --right ${ ','.join(['"%s"' % x for x in $inputs.right_input]) } + + #if $inputs.left_input[0].is_of_type('fasta'): --seqType fa #else: --seqType fq #end if - + #if $inputs.strand.is_strand_specific: --SS_lib_type $inputs.strand.library_type #end if - + $inputs.jaccard_clip #else: - --single $inputs.input - - #if $inputs.input.is_of_type('fasta'): + --single ${ ','.join(['"%s"' % x for x in $inputs.input]) } + + #if $inputs.input[0].is_of_type('fasta'): --seqType fa #else: --seqType fq #end if - + #if $inputs.strand.is_strand_specific: --SS_lib_type $inputs.strand.library_type #end if #end if - + $norm ## Additional parameters. @@ -58,12 +61,12 @@ #if $additional_params.guided.genome_guided_min_reads_per_partition: --genome_guided_min_reads_per_partition $additional_params.guided.genome_guided_min_reads_per_partition #end if - + #end if ## CPU and butterfly options. --CPU \${GALAXY_SLOTS:-4} \${TRINITY_MEM_OPTIONS:---max_memory 1G} --bfly_opts "-V 10 --stderr" - + ## > $trinity_log 2>&1 ]]></command> @@ -74,8 +77,8 @@ <option value="single">Single</option> </param> <when value="paired"> - <param format="fasta,fastqsanger" name="left_input" type="data" label="Left/Forward strand reads" help=""/> - <param format="fasta,fastqsanger" name="right_input" type="data" label="Right/Reverse strand reads" help=""/> + <param format="fasta,fastqsanger" name="left_input" multiple="true" type="data" label="Left/Forward strand reads" help=""/> + <param format="fasta,fastqsanger" name="right_input" multiple="true" type="data" label="Right/Reverse strand reads" help=""/> <conditional name="strand"> <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/> <when value="false"> @@ -90,7 +93,7 @@ <param name="jaccard_clip" type="boolean" truevalue="--jaccard_clip" falsevalue="" checked="false" label="Jaccard Clip options" help="set if you expect high gene density with UTR overlap"/> </when> <when value="single"> - <param format="fasta,fastqsanger" name="input" type="data" label="Single-end reads" help=""/> + <param format="fasta,fastqsanger" name="input" multiple="true" type="data" label="Single-end reads" help=""/> <conditional name="strand"> <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/> <when value="false"> @@ -104,12 +107,12 @@ </conditional> </when> </conditional> - + <param name="norm" type="boolean" 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" type="integer" optional="true" value="200" min="1" label="Minimum Contig Length" help="All contigs shorter than this will be discarded"/> - + <conditional name="guided"> <param name="is_guided" type="select" label="Use the genome guided mode?" help="If you already mapped the reads to the genome, Trinity can use this information"> <option value="no">No</option> @@ -123,8 +126,8 @@ <param name="genome_guided_min_reads_per_partition" type="integer" optional="true" value="10" min="1" label="Minimum number of reads per partition"/> </when> </conditional> - - + + <param format="fasta" name="long_reads" type="data" optional="true" label="Error-corrected or circular consensus (CCS) pac bio reads" help="Experimental feature! Long reads must be in the same orientation as short reads if they are strand specific"/> </section> </inputs> @@ -135,8 +138,8 @@ <tests> <test> <param name="paired_or_single" value="paired"/> - <param name="left_input" value="reads.left.fq"/> - <param name="right_input" value="reads.right.fq"/> + <param name="left_input" value="reads.left.fq" ftype="fastqsanger"/> + <param name="right_input" value="reads.right.fq" ftype="fastqsanger"/> <param name="is_strand_specific" value="true"/> <param name="norm" value="false"/> <param name="library_type" value="RF"/> @@ -144,8 +147,8 @@ </test> <test> <param name="paired_or_single" value="paired"/> - <param name="left_input" value="reads.left.fq"/> - <param name="right_input" value="reads.right.fq"/> + <param name="left_input" value="reads.left.fq" ftype="fastqsanger"/> + <param name="right_input" value="reads.right.fq" ftype="fastqsanger"/> <param name="is_strand_specific" value="true"/> <param name="norm" value="true"/> <param name="library_type" value="RF"/> @@ -157,7 +160,7 @@ .. _Trinity: http://trinityrnaseq.github.io </help> - + <citations> <citation type="doi">doi:10.1038/nbt.1883</citation> </citations> |