commit/galaxy-central: 3 new changesets
3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/16e5c3e19479/ Changeset: 16e5c3e19479 User: raj76 Date: 2013-04-01 22:59:55 Summary: Changed the logic in the trinity wrapper to handle stranded/un-stranded ran-seq data. Got the wrapper working with the latest trinity package. Affected #: 1 file diff -r b167cc662167404c49b3ff0a9535f448669d93d5 -r 16e5c3e1947986102b11fe050691c722ba923696 tools/ngs_rna/trinity_all.xml --- a/tools/ngs_rna/trinity_all.xml +++ b/tools/ngs_rna/trinity_all.xml @@ -20,9 +20,6 @@ #else: --seqType fq #end if - #if $inputs.library_type != 'None': - --SS_lib_type $inputs.library_type - #end if #else: --single $inputs.input #if $inputs.input.ext == 'fa': @@ -30,15 +27,16 @@ #else: --seqType fq #end if - #if $inputs.library_type != 'None': - --SS_lib_type $inputs.library_type - #end if + #end if + + #if $strand.is_strand_specific == "yes": + --SS_lib_type $strand.library_type #end if - --kmer_method meryl - + --JM 100G --full_cleanup + ## CPU and butterfly options. - --CPU 4 --bfly_opts "-V 10 --stderr" > $trinity_log 2>&1 + --CPU 6 --bfly_opts "-V 10 --stderr" > $trinity_log 2>&1 </command><inputs><conditional name="inputs"> @@ -49,22 +47,28 @@ <when value="paired"><param format="fasta,fastq" name="left_input" type="data" label="Left/Forward strand reads" help=""/><param format="fasta,fastq" name="right_input" type="data" label="Right/Reverse strand reads" help=""/> - <param name="library_type" type="select" label="Strand-specific Library Type"> - <option value="None">None</option> - <option value="FR">FR</option> - <option value="RF">RF</option> - </param><param name="paired_fragment_length" type="integer" value="300" min="1" label="Paired Fragment Length" help="Maximum length expected between fragment pairs"/></when><when value="single"><param format="fasta,fastq" name="input" type="data" label="Single-end reads" help=""/> - <param name="library_type" type="select" label="Strand-specific Library Type"> - <option value="None">None</option> - <option value="F">F</option> - <option value="R">R</option> - </param></when></conditional> + <conditional name="strand"> + <param name="is_strand_specific" type="select" label="Is it strand specific data?" help=""> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <when value="no"> + </when> + <when value="yes"> + <param name="library_type" type="select" label="Strand-specific Library Type"> + <option value="FR">Forward-Reverse</option> + <option value="RF">Reverse-Forward</option> + <option value="F">Forward</option> + <option value="R">Reverse</option> + </param> + </when> + </conditional><conditional name="additional_params"><param name="use_additional" type="select" label="Use Additional Params?"><option value="no">No</option> @@ -79,7 +83,7 @@ </inputs><outputs><data format="txt" name="trinity_log" label="${tool.name} on ${on_string}: log" /> - <data format="fasta" name="assembled_transcripts" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir/Trinity.fasta"/> + <data format="fasta" name="assembled_transcripts" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir.Trinity.fasta"/></outputs><tests></tests> https://bitbucket.org/galaxy/galaxy-central/commits/663cc29efad9/ Changeset: 663cc29efad9 User: raj76 Date: 2013-04-04 07:16:09 Summary: Removed --full_cleanup as galaxy deletes the job's working directory. Changed the memory for Jellyfish to 10G from 100G. Probably better as a default value. Affected #: 1 file diff -r 16e5c3e1947986102b11fe050691c722ba923696 -r 663cc29efad9ec1a54bfc108b6be7e34a1dc6b17 tools/ngs_rna/trinity_all.xml --- a/tools/ngs_rna/trinity_all.xml +++ b/tools/ngs_rna/trinity_all.xml @@ -33,7 +33,7 @@ --SS_lib_type $strand.library_type #end if - --JM 100G --full_cleanup + --JM 10G ## CPU and butterfly options. --CPU 6 --bfly_opts "-V 10 --stderr" > $trinity_log 2>&1 @@ -83,7 +83,7 @@ </inputs><outputs><data format="txt" name="trinity_log" label="${tool.name} on ${on_string}: log" /> - <data format="fasta" name="assembled_transcripts" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir.Trinity.fasta"/> + <data format="fasta" name="assembled_transcripts" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir/Trinity.fasta"/></outputs><tests></tests> https://bitbucket.org/galaxy/galaxy-central/commits/c43fff394fd0/ Changeset: c43fff394fd0 User: jgoecks Date: 2013-04-04 15:13:18 Summary: Merged in raj76/galaxy-central-tools (pull request #147) Changed the logic in the trinity wrapper to handle stranded/un-stranded ran-seq data. Got the wrapper working with the latest trinity package. Affected #: 1 file diff -r c7fae25b9fa35533afb15df6a6fdb47d677f8110 -r c43fff394fd02f868d3c8c669344c0f0870fdaa9 tools/ngs_rna/trinity_all.xml --- a/tools/ngs_rna/trinity_all.xml +++ b/tools/ngs_rna/trinity_all.xml @@ -20,9 +20,6 @@ #else: --seqType fq #end if - #if $inputs.library_type != 'None': - --SS_lib_type $inputs.library_type - #end if #else: --single $inputs.input #if $inputs.input.ext == 'fa': @@ -30,15 +27,16 @@ #else: --seqType fq #end if - #if $inputs.library_type != 'None': - --SS_lib_type $inputs.library_type - #end if + #end if + + #if $strand.is_strand_specific == "yes": + --SS_lib_type $strand.library_type #end if - --kmer_method meryl - + --JM 10G + ## CPU and butterfly options. - --CPU 4 --bfly_opts "-V 10 --stderr" > $trinity_log 2>&1 + --CPU 6 --bfly_opts "-V 10 --stderr" > $trinity_log 2>&1 </command><inputs><conditional name="inputs"> @@ -49,22 +47,28 @@ <when value="paired"><param format="fasta,fastq" name="left_input" type="data" label="Left/Forward strand reads" help=""/><param format="fasta,fastq" name="right_input" type="data" label="Right/Reverse strand reads" help=""/> - <param name="library_type" type="select" label="Strand-specific Library Type"> - <option value="None">None</option> - <option value="FR">FR</option> - <option value="RF">RF</option> - </param><param name="paired_fragment_length" type="integer" value="300" min="1" label="Paired Fragment Length" help="Maximum length expected between fragment pairs"/></when><when value="single"><param format="fasta,fastq" name="input" type="data" label="Single-end reads" help=""/> - <param name="library_type" type="select" label="Strand-specific Library Type"> - <option value="None">None</option> - <option value="F">F</option> - <option value="R">R</option> - </param></when></conditional> + <conditional name="strand"> + <param name="is_strand_specific" type="select" label="Is it strand specific data?" help=""> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <when value="no"> + </when> + <when value="yes"> + <param name="library_type" type="select" label="Strand-specific Library Type"> + <option value="FR">Forward-Reverse</option> + <option value="RF">Reverse-Forward</option> + <option value="F">Forward</option> + <option value="R">Reverse</option> + </param> + </when> + </conditional><conditional name="additional_params"><param name="use_additional" type="select" label="Use Additional Params?"><option value="no">No</option> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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