| Previous changeset 5:407b894abb08 (2016-11-03) |
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Commit message:
planemo upload for repository https://bitbucket.org/crs4/orione-tools/src/bb-orione-tools/custom/edge_pro/ commit 02541df6373bc61be0cdc0617c8549cf8b49b832 |
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modified:
edge_pro.xml |
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| diff -r 407b894abb08 -r e6e6f5f9b9c4 edge_pro.xml --- a/edge_pro.xml Thu Nov 03 10:56:44 2016 -0400 +++ b/edge_pro.xml Thu Aug 31 12:54:08 2017 -0400 |
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| b'@@ -1,110 +1,99 @@\n-<tool id="edge_pro" name="EDGE-pro" version="1.0.1">\n- <description>Gene expression in Prokaryotes</description>\n- <requirements>\n- <requirement type="package" version="2.1.0">bowtie2</requirement>\n- <requirement type="package" version="1.3.1">edge-pro</requirement>\n- </requirements>\n- <command>\n- edge.pl -t \\${GALAXY_SLOTS:-4} -o edge_out\n- ## Mandatory input parameters\n- -g $genome\n- -p $ptt\n- -r $rnt\n+<tool id="edge_pro" name="EDGE-pro" version="1.0.2">\n+ <description>Gene expression in Prokaryotes</description>\n+ <requirements>\n+ <requirement type="package" version="2.1.0">bowtie2</requirement>\n+ <requirement type="package" version="1.3.1">edge-pro</requirement>\n+ </requirements>\n+ <command detect_errors="exit_code"><![CDATA[\n+edge.pl -t \\${GALAXY_SLOTS:-4} -o edge_out\n+## Mandatory input parameters\n+-g \'$genome\'\n+-p \'$ptt\'\n+-r \'$rnt\'\n \n- #if $singlePaired.sPaired == "single"\n- -u $singlePaired.input1\n- #else if $singlePaired.sPaired == "paired"\n- -u $singlePaired.input1\n- -v $singlePaired.input2\n- #else if $singlePaired.sPaired == "pairedCollection"\n- -u $singlePaired.input.forward\n- -v $singlePaired.input.reverse\n- #end if\n+#if $singlePaired.sPaired == "single"\n+ -u \'$singlePaired.input1\'\n+#else if $singlePaired.sPaired == "paired"\n+ -u \'$singlePaired.input1\'\n+ -v \'$singlePaired.input2\'\n+#else if $singlePaired.sPaired == "pairedCollection"\n+ -u \'$singlePaired.input.forward\'\n+ -v \'$singlePaired.input.reverse\'\n+#end if\n+\n+#if $singlePaired.sPaired in ("paired", "pairedCollection")\n+ #if str($singlePaired.minInsertSize)\n+ -m $singlePaired.minInsertSize\n+ #end if\n+ #if str($singlePaired.maxInsertSize)\n+ -M $singlePaired.maxInsertSize\n+ #end if\n+#end if\n \n- #if $singlePaired.sPaired in ["paired", "pairedCollection"]\n- #if str($singlePaired.minInsertSize)\n- -m $singlePaired.minInsertSize\n- #end if\n- #if str($singlePaired.maxInsertSize)\n- -M $singlePaired.maxInsertSize\n- #end if\n- #end if\n- \n- ## Optional input parameters\n- #if $params.settingsType == "full"\n- #if str($params.window)\n- -w $params.window\n- #end if\n- #if str($params.utrSize)\n- -i $params.utrSize\n- #end if\n- #if str($params.similarity)\n- -x $params.similarity\n- #end if\n- #if str($params.readLength)\n- -l $params.readLength\n- #end if\n- #if str($params.minCoverage)\n- -c $params.minCoverage\n- #end if\n- #end if\n- > $out_log 2>&1 ## need to redirect stderr because edge.pl calls bowtie2 and count which write some logging info there\n- && cat edge_out.rpkm_* > $out_rpkm\n- </command>\n- <stdio>\n- <exit_code range="1:" level="fatal" />\n- </stdio>\n- <inputs>\n- <conditional name="singlePaired">\n- <param name="sPaired" type="select" label="Is this library mate-paired?">\n- <option value="single">Single-end</option>\n- <option value="paired">Paired-end</option>\n- <option value="pairedCollection">Paired-end collection</option>\n- </param>\n- <when value="single">\n- <param format="fastqsanger" name="input1" type="data" label="FASTQ file" help="FASTQ format with Sanger-scaled quality values (Galaxy fastqsanger datatype)"/>\n- </when>\n- <when value="paired">\n- <param format="fastqsanger" name="input1" type="data" label="Forward FASTQ file" help="FASTQ format with Sanger-scaled quality values (Galaxy fastqsanger datatype)" />\n- <param format="fastqsanger" name="input2" type="data" label="Reverse FASTQ file" help="FASTQ format with Sanger-scaled quality values (Galaxy fastqsanger datatype)" />\n- <param name="minInsertSize" type="integer" optional="true" min="0" value="0" label="Minimun insert size in paired-end library for Bowtie2 (-m)" />\n- <param name="maxInsertSize" type="integer" optional="true" min="1" value="500" la'..b' with coordinates of coding genes" />\n+ <param name="rnt" argument="-r" type="data" format="rnt" label="Coordinates of structural RNAs (RNT file)" help="RNT file with coordinates of structural RNA" />\n \n- <help>\n+ <section name="params" title="Advanced parameters" expanded="false">\n+ <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" />\n+ <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" />\n+ <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" />\n+ <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" />\n+ <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" />\n+ </section>\n+ </inputs>\n \n+ <outputs>\n+ <data name="out_aln" format="sam" label="${tool.name} on ${on_string}: alignment" from_work_dir="edge_out.alignments" />\n+ <data name="out_rpkm" format="tabular" label="${tool.name} on ${on_string}: rpkm"/>\n+ <data name="out_log" format="txt" label="${tool.name} on ${on_string}: log"/>\n+ </outputs>\n+\n+ <help><![CDATA[\n **What it does**\n \n `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.\n@@ -117,7 +106,7 @@\n 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`_.\n This tool accepts files in Sanger FASTQ format (Galaxy *fastqsanger* datatype). Use the FASTQ Groomer tool to prepare your files.\n \n-.. _NCBI ftp repository: ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/\n+.. _NCBI ftp repository: ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/bacteria/\n \n .. class:: warningmark\n \n@@ -128,20 +117,14 @@\n This Galaxy tool is Copyright \xc2\xa9 2012-2014 `CRS4 Srl.`_ and is released under the `MIT license`_.\n \n .. _CRS4 Srl.: http://www.crs4.it/\n-.. _MIT license: http://opensource.org/licenses/MIT\n+.. _MIT license: https://opensource.org/licenses/MIT\n \n You can use this tool only if you agree to the license terms of: `EDGE-pro`_.\n \n .. _EDGE-pro: http://ccb.jhu.edu/software/EDGE-pro/\n-\n-If you use this tool, please cite:\n-\n-- |Cuccuru2014|_\n-- |Magoc2013|_.\n-\n-.. |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\n-.. _Cuccuru2014: http://bioinformatics.oxfordjournals.org/content/30/13/1928\n-.. |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\n-.. _Magoc2013: http://www.la-press.com/edge-pro-estimated-degree-of-gene-expression-in-prokaryotic-genomes-article-a3586\n- </help>\n+ ]]></help>\n+ <citations>\n+ <citation type="doi">10.4137/EBO.S11250</citation>\n+ <citation type="doi">10.1093/bioinformatics/btu135</citation>\n+ </citations>\n </tool>\n' |