Mercurial > repos > crs4 > edge_pro
changeset 6:e6e6f5f9b9c4 draft default tip
planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832
| author | crs4 |
|---|---|
| date | Thu, 31 Aug 2017 12:54:08 -0400 |
| parents | 407b894abb08 |
| children | |
| files | edge_pro.xml |
| diffstat | 1 files changed, 98 insertions(+), 115 deletions(-) [+] |
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--- a/edge_pro.xml Thu Nov 03 10:56:44 2016 -0400 +++ b/edge_pro.xml Thu Aug 31 12:54:08 2017 -0400 @@ -1,110 +1,99 @@ -<tool id="edge_pro" name="EDGE-pro" version="1.0.1"> - <description>Gene expression in Prokaryotes</description> - <requirements> - <requirement type="package" version="2.1.0">bowtie2</requirement> - <requirement type="package" version="1.3.1">edge-pro</requirement> - </requirements> - <command> - edge.pl -t \${GALAXY_SLOTS:-4} -o edge_out - ## Mandatory input parameters - -g $genome - -p $ptt - -r $rnt +<tool id="edge_pro" name="EDGE-pro" version="1.0.2"> + <description>Gene expression in Prokaryotes</description> + <requirements> + <requirement type="package" version="2.1.0">bowtie2</requirement> + <requirement type="package" version="1.3.1">edge-pro</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ +edge.pl -t \${GALAXY_SLOTS:-4} -o edge_out +## Mandatory input parameters +-g '$genome' +-p '$ptt' +-r '$rnt' - #if $singlePaired.sPaired == "single" - -u $singlePaired.input1 - #else if $singlePaired.sPaired == "paired" - -u $singlePaired.input1 - -v $singlePaired.input2 - #else if $singlePaired.sPaired == "pairedCollection" - -u $singlePaired.input.forward - -v $singlePaired.input.reverse - #end if +#if $singlePaired.sPaired == "single" + -u '$singlePaired.input1' +#else if $singlePaired.sPaired == "paired" + -u '$singlePaired.input1' + -v '$singlePaired.input2' +#else if $singlePaired.sPaired == "pairedCollection" + -u '$singlePaired.input.forward' + -v '$singlePaired.input.reverse' +#end if + +#if $singlePaired.sPaired in ("paired", "pairedCollection") + #if str($singlePaired.minInsertSize) + -m $singlePaired.minInsertSize + #end if + #if str($singlePaired.maxInsertSize) + -M $singlePaired.maxInsertSize + #end if +#end if - #if $singlePaired.sPaired in ["paired", "pairedCollection"] - #if str($singlePaired.minInsertSize) - -m $singlePaired.minInsertSize - #end if - #if str($singlePaired.maxInsertSize) - -M $singlePaired.maxInsertSize - #end if - #end if - - ## Optional input parameters - #if $params.settingsType == "full" - #if str($params.window) - -w $params.window - #end if - #if str($params.utrSize) - -i $params.utrSize - #end if - #if str($params.similarity) - -x $params.similarity - #end if - #if str($params.readLength) - -l $params.readLength - #end if - #if str($params.minCoverage) - -c $params.minCoverage - #end if - #end if - > $out_log 2>&1 ## need to redirect stderr because edge.pl calls bowtie2 and count which write some logging info there - && cat edge_out.rpkm_* > $out_rpkm - </command> - <stdio> - <exit_code range="1:" level="fatal" /> - </stdio> - <inputs> - <conditional name="singlePaired"> - <param name="sPaired" type="select" label="Is this library mate-paired?"> - <option value="single">Single-end</option> - <option value="paired">Paired-end</option> - <option value="pairedCollection">Paired-end collection</option> - </param> - <when value="single"> - <param format="fastqsanger" name="input1" type="data" label="FASTQ file" help="FASTQ format with Sanger-scaled quality values (Galaxy fastqsanger datatype)"/> - </when> - <when value="paired"> - <param format="fastqsanger" name="input1" type="data" label="Forward FASTQ file" help="FASTQ format with Sanger-scaled quality values (Galaxy fastqsanger datatype)" /> - <param format="fastqsanger" name="input2" type="data" label="Reverse FASTQ file" help="FASTQ format with Sanger-scaled quality values (Galaxy fastqsanger datatype)" /> - <param name="minInsertSize" type="integer" optional="true" min="0" value="0" label="Minimun insert size in paired-end library for Bowtie2 (-m)" /> - <param name="maxInsertSize" type="integer" optional="true" min="1" value="500" label="Maximun insert size in paired-end library for Bowtie2 (-M)" /> - </when> - <when value="pairedCollection"> - <param format="fastqsanger" name="input" type="data_collection" collection_type="paired" label="FASTQ paired collection" help="FASTQ format with Sanger-scaled quality values (Galaxy fastqsanger datatype)" /> - <param name="minInsertSize" type="integer" optional="true" min="0" value="0" label="Minimun insert size in paired-end library for Bowtie2 (-m)" /> - <param name="maxInsertSize" type="integer" optional="true" min="1" value="500" label="Maximun insert size in paired-end library for Bowtie2 (-M)" /> - </when> - </conditional> - - <param format="fasta" name="genome" type="data" label="Select the reference genome from your history (-g)" help="FASTA format" /> - <param format="ptt" name="ptt" type="data" label="Coordinates of coding genes (PTT file)" help="PTT file with coordinates of coding genes (-p)" /> - <param format="rnt" name="rnt" type="data" label="Coordinates of structural RNAs (RNT file)" help="RNT file with coordinates of structural RNA (-r)" /> - - <conditional name="params"> - <param name="settingsType" type="select" label="Parameter settings" help="For most needs, use default settings. If you want full control use Full Parameter List"> - <option value="preSet">Use defaults</option> - <option value="full">Full parameter list</option> - </param> - <when value="preSet" /> - <when value="full"> - <param name="window" type="integer" optional="true" value="100" label="Window length for coverage distribution (-w)" help="Used to distribute the coverage between two overlapping genes. See help below for details" /> - <param name="utrSize" type="integer" optional="true" value="40" label="Size of the untranslated region (-i)" help="Enter the size of the untranslated region between the initial transcription site and the start codon" /> - <param name="similarity" type="float" optional="true" value="0.15" label="Percentage for similar coverage (-x)" help="Enter the percentage used to determine when two coverage values are considered similar. See help below for details" /> - <param name="readLength" type="integer" optional="true" value="" label="Read length (-l)" help="If not specified, the first 1000 reads are used to approximate the read length" /> - <param name="minCoverage" type="integer" optional="true" value="3" label="Minimum average coverage for expressed genes (-c)" help="Coverage less than specified is assumed to be noise and gene is considered to not be expressed" /> - </when> - </conditional> - </inputs> +## Optional input parameters +#if $params.settingsType == "full" + #if str($params.window) + -w $params.window + #end if + #if str($params.utrSize) + -i $params.utrSize + #end if + #if str($params.similarity) + -x $params.similarity + #end if + #if str($params.readLength) + -l $params.readLength + #end if + #if str($params.minCoverage) + -c $params.minCoverage + #end if +#end if +> '$out_log' 2>&1 ## need to redirect stderr because edge.pl calls bowtie2 and count which write some logging info there +&& cat edge_out.rpkm_* > '$out_rpkm' + ]]></command> + <inputs> + <conditional name="singlePaired"> + <param name="sPaired" type="select" label="Is this library mate-paired?"> + <option value="single">Single-end</option> + <option value="paired">Paired-end</option> + <option value="pairedCollection">Paired-end collection</option> + </param> + <when value="single"> + <param name="input1" type="data" format="fastqsanger" label="FASTQ file" help="FASTQ format with Sanger-scaled quality values (Galaxy fastqsanger datatype)"/> + </when> + <when value="paired"> + <param name="input1" type="data" format="fastqsanger" label="Forward FASTQ file" help="FASTQ format with Sanger-scaled quality values (Galaxy fastqsanger datatype)" /> + <param name="input2" type="data" format="fastqsanger" label="Reverse FASTQ file" help="FASTQ format with Sanger-scaled quality values (Galaxy fastqsanger datatype)" /> + <param name="minInsertSize" argument="-m" type="integer" optional="true" min="0" value="0" label="Minimun insert size in paired-end library for Bowtie2" /> + <param name="maxInsertSize" argument="-M" type="integer" optional="true" min="1" value="500" label="Maximun insert size in paired-end library for Bowtie2" /> + </when> + <when value="pairedCollection"> + <param name="input" type="data_collection" collection_type="paired" format="fastqsanger" label="FASTQ paired collection" help="FASTQ format with Sanger-scaled quality values (Galaxy fastqsanger datatype)" /> + <param name="minInsertSize" argument="-m" type="integer" optional="true" min="0" value="0" label="Minimun insert size in paired-end library for Bowtie2" /> + <param name="maxInsertSize" argument="-M" type="integer" optional="true" min="1" value="500" label="Maximun insert size in paired-end library for Bowtie2" /> + </when> + </conditional> - <outputs> - <data format="sam" name="out_aln" label="${tool.name} on ${on_string}: alignment" from_work_dir="edge_out.alignments" /> - <data format="tabular" name="out_rpkm" label="${tool.name} on ${on_string}: rpkm"/> - <data format="txt" name="out_log" label="${tool.name} on ${on_string}: log"/> - </outputs> + <param name="genome" argument="-g" type="data" format="fasta" label="Select the reference genome from your history" help="In FASTA format" /> + <param name="ptt" argument="-p" type="data" format="ptt" label="Coordinates of coding genes (PTT file)" help="PTT file with coordinates of coding genes" /> + <param name="rnt" argument="-r" type="data" format="rnt" label="Coordinates of structural RNAs (RNT file)" help="RNT file with coordinates of structural RNA" /> - <help> + <section name="params" title="Advanced parameters" expanded="false"> + <param name="window" argument="-w" type="integer" optional="true" value="100" label="Window length for coverage distribution" help="Used to distribute the coverage between two overlapping genes. See help below for details" /> + <param name="utrSize" argument="-i" type="integer" optional="true" value="40" label="Size of the untranslated region" help="Enter the size of the untranslated region between the initial transcription site and the start codon" /> + <param name="similarity" argument="-x" type="float" optional="true" value="0.15" label="Percentage for similar coverage" help="Enter the percentage used to determine when two coverage values are considered similar. See help below for details" /> + <param name="readLength" argument="-l" type="integer" optional="true" value="" label="Read length" help="If not specified, the first 1000 reads are used to approximate the read length" /> + <param name="minCoverage" argument="-c" type="integer" optional="true" value="3" label="Minimum average coverage for expressed genes" help="Coverage less than specified is assumed to be noise and gene is considered to not be expressed" /> + </section> + </inputs> + <outputs> + <data name="out_aln" format="sam" label="${tool.name} on ${on_string}: alignment" from_work_dir="edge_out.alignments" /> + <data name="out_rpkm" format="tabular" label="${tool.name} on ${on_string}: rpkm"/> + <data name="out_log" format="txt" label="${tool.name} on ${on_string}: log"/> + </outputs> + + <help><![CDATA[ **What it does** `EDGE-pro`_, Estimated Degree of Gene Expression in PROkaryots is an efficient software system to estimate gene expression levels in prokaryotic genomes from RNA-seq data. EDGE-pro uses Bowtie2 for alignment and then estimates expression directly from the alignment results. @@ -117,7 +106,7 @@ Input files with gene coordinates in PTT and RNT format can be retrieved with the Get EDGE-pro Files tool available in Galaxy, or downloaded from the `NCBI ftp repository`_. This tool accepts files in Sanger FASTQ format (Galaxy *fastqsanger* datatype). Use the FASTQ Groomer tool to prepare your files. -.. _NCBI ftp repository: ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/ +.. _NCBI ftp repository: ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/bacteria/ .. class:: warningmark @@ -128,20 +117,14 @@ This Galaxy tool is Copyright © 2012-2014 `CRS4 Srl.`_ and is released under the `MIT license`_. .. _CRS4 Srl.: http://www.crs4.it/ -.. _MIT license: http://opensource.org/licenses/MIT +.. _MIT license: https://opensource.org/licenses/MIT You can use this tool only if you agree to the license terms of: `EDGE-pro`_. .. _EDGE-pro: http://ccb.jhu.edu/software/EDGE-pro/ - -If you use this tool, please cite: - -- |Cuccuru2014|_ -- |Magoc2013|_. - -.. |Cuccuru2014| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2014) Orione, a web-based framework for NGS analysis in microbiology. *Bioinformatics* 30(13), 1928-1929 -.. _Cuccuru2014: http://bioinformatics.oxfordjournals.org/content/30/13/1928 -.. |Magoc2013| replace:: Magoc, T., Wood, D., Salzberg, S. L. (2013) EDGE-pro: Estimated Degree of Gene Expression in Prokaryotic Genomes. *Evol. Bioinform.* 2013:9, 127-136 -.. _Magoc2013: http://www.la-press.com/edge-pro-estimated-degree-of-gene-expression-in-prokaryotic-genomes-article-a3586 - </help> + ]]></help> + <citations> + <citation type="doi">10.4137/EBO.S11250</citation> + <citation type="doi">10.1093/bioinformatics/btu135</citation> + </citations> </tool>