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comparison edge_pro.xml @ 2:bad8a51514dd draft

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Directly call edge.pl, remove edge_pro.py . Move minimun and maximum insert size params to paired library section. Update Orione citation.
author crs4
date Wed, 05 Mar 2014 06:44:35 -0500
parents f77ce4f92b46
children ddcbf8732706
comparison
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1:f77ce4f92b46 2:bad8a51514dd
1 <tool id="edge_pro" name="EDGE-pro" version="1.0.0"> 1 <tool id="edge_pro" name="EDGE-pro" version="1.0.1">
2 <description>Gene expression in Prokaryotes</description> 2 <description>Gene expression in Prokaryotes</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.1.0">bowtie2</requirement> 4 <requirement type="package" version="2.1.0">bowtie2</requirement>
5 <requirement type="package" version="1.3.1">edge-pro</requirement> 5 <requirement type="package" version="1.3.1">edge-pro</requirement>
6 </requirements> 6 </requirements>
7 <command interpreter="python"> 7 <command>
8 edge_pro.py 8 edge.pl -t \${GALAXY_SLOTS:-4} -o edge_out
9 --num-threads=\${GALAXY_SLOTS:-4}
10
11 ## Mandatory input parameters 9 ## Mandatory input parameters
12 --genome $genome 10 -g $genome
13 --ptt $ptt 11 -p $ptt
14 --rnt $rnt 12 -r $rnt
15 ## First input file always required 13 ## First input file always required
16 --input1 $singlePaired.input1 14 -u $singlePaired.input1
17 ## Second input only if input is paired-end 15 ## Second input only if input is paired-end
18 #if $singlePaired.sPaired == "paired" 16 #if $singlePaired.sPaired == "paired"
19 --input2=$singlePaired.input2 17 -v $singlePaired.input2
18 #if str($singlePaired.minInsertSize)
19 -m $singlePaired.minInsertSize
20 #end if
21 #if str($singlePaired.maxInsertSize)
22 -M $singlePaired.maxInsertSize
23 #end if
20 #end if 24 #end if
21 25
22 ## Optional input parameters 26 ## Optional input parameters
23 #if $params.settingsType == "full" 27 #if $params.settingsType == "full"
24 #if str($params.minInsertSize)
25 --minInsertSize=$params.minInsertSize
26 #end if
27 #if str($params.maxInsertSize)
28 --maxInsertSize=$params.maxInsertSize
29 #end if
30 #if str($params.window) 28 #if str($params.window)
31 --window=$params.window 29 -w $params.window
32 #end if 30 #end if
33 #if str($params.utrSize) 31 #if str($params.utrSize)
34 --utrSize=$params.utrSize 32 -i $params.utrSize
35 #end if 33 #end if
36 #if str($params.similarity) 34 #if str($params.similarity)
37 --similarity=$params.similarity 35 -x $params.similarity
38 #end if 36 #end if
39 #if str($params.readLength) 37 #if str($params.readLength)
40 --readLength=$params.readLength 38 -l $params.readLength
41 #end if 39 #end if
42 #if str($params.minCoverage) 40 #if str($params.minCoverage)
43 --minCoverage=$params.minCoverage 41 -c $params.minCoverage
44 #end if 42 #end if
45 #end if 43 #end if
46 44 &gt; $out_log 2&gt;&amp;1 ## need to redirect stderr because edge.pl calls bowtie2 and count which write some logging info there
47 ## Outputs 45 &amp;&amp; cat edge_out.rpkm_* > $out_rpkm
48 --out-aln $out_aln
49 --out-rpkm $out_rpkm
50 --out-log $out_log
51 </command> 46 </command>
47 <stdio>
48 <exit_code range="1:" level="fatal" />
49 </stdio>
52 <inputs> 50 <inputs>
53 <conditional name="singlePaired"> 51 <conditional name="singlePaired">
54 <param name="sPaired" type="select" label="Is this library mate-paired?"> 52 <param name="sPaired" type="select" label="Is this library mate-paired?">
55 <option value="single">Single-end</option> 53 <option value="single">Single-end</option>
56 <option value="paired">Paired-end</option> 54 <option value="paired">Paired-end</option>
59 <param format="fastqsanger" name="input1" type="data" label="FASTQ file" help="FASTQ format with Sanger-scaled quality values (Galaxy fastqsanger datatype)"/> 57 <param format="fastqsanger" name="input1" type="data" label="FASTQ file" help="FASTQ format with Sanger-scaled quality values (Galaxy fastqsanger datatype)"/>
60 </when> 58 </when>
61 <when value="paired"> 59 <when value="paired">
62 <param format="fastqsanger" name="input1" type="data" label="Forward FASTQ file" help="FASTQ format with Sanger-scaled quality values (Galaxy fastqsanger datatype)" /> 60 <param format="fastqsanger" name="input1" type="data" label="Forward FASTQ file" help="FASTQ format with Sanger-scaled quality values (Galaxy fastqsanger datatype)" />
63 <param format="fastqsanger" name="input2" type="data" label="Reverse FASTQ file" help="FASTQ format with Sanger-scaled quality values (Galaxy fastqsanger datatype)" /> 61 <param format="fastqsanger" name="input2" type="data" label="Reverse FASTQ file" help="FASTQ format with Sanger-scaled quality values (Galaxy fastqsanger datatype)" />
62 <param name="minInsertSize" type="integer" optional="true" min="0" value="0" label="Minimun insert size in paired-end library for Bowtie2 (-m)" />
63 <param name="maxInsertSize" type="integer" optional="true" min="1" value="500" label="Maximun insert size in paired-end library for Bowtie2 (-M)" />
64 </when> 64 </when>
65 </conditional> 65 </conditional>
66 66
67 <param format="fasta" name="genome" type="data" label="Select the reference genome from your history (-g)" help="FASTA format" /> 67 <param format="fasta" name="genome" type="data" label="Select the reference genome from your history (-g)" help="FASTA format" />
68 <param format="ptt" name="ptt" type="data" label="Coordinates of coding genes (PTT file)" help="PTT file with coordinates of coding genes (-p)" /> 68 <param format="ptt" name="ptt" type="data" label="Coordinates of coding genes (PTT file)" help="PTT file with coordinates of coding genes (-p)" />
69 <param format="rnt" name="rnt" type="data" label="Coordinates of structural RNAs (RNT file)" help="RNT file with coordinates of structural RNA (-r)" /> 69 <param format="rnt" name="rnt" type="data" label="Coordinates of structural RNAs (RNT file)" help="RNT file with coordinates of structural RNA (-r)" />
70 70
71 <conditional name="params"> 71 <conditional name="params">
72 <param name="settingsType" type="select" label="Parameter settings" help="For most needs, use default settings. If you want full control use Full Parameter List"> 72 <param name="settingsType" type="select" label="Parameter settings" help="For most needs, use default settings. If you want full control use Full Parameter List">
73 <option value="preSet">Use Defaults</option> 73 <option value="preSet">Use defaults</option>
74 <option value="full">Full parameter list</option> 74 <option value="full">Full parameter list</option>
75 </param> 75 </param>
76 <when value="preSet" /> 76 <when value="preSet" />
77 <!-- Full/advanced params. -->
78 <when value="full"> 77 <when value="full">
79 <param name="minInsertSize" type="integer" optional="true" value="0" label="Minimun insert size for a read pair (-m)" help="For paired-end reads only" />
80 <param name="maxInsertSize" type="integer" optional="true" value="500" label="Maximun insert size for a read pair (-M)" help="For paired-end reads only" />
81 <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" /> 78 <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" />
82 <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" /> 79 <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" />
83 <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" /> 80 <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" />
84 <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" /> 81 <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" />
85 <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" /> 82 <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" />
86 </when> <!-- full --> 83 </when>
87 </conditional> 84 </conditional>
88 </inputs> 85 </inputs>
89 86
90 <outputs> 87 <outputs>
91 <data format="sam" name="out_aln" label="${tool.name} on ${on_string}: alignment"/> 88 <data format="sam" name="out_aln" label="${tool.name} on ${on_string}: alignment" from_work_dir="edge_out.alignments" />
92 <data format="tabular" name="out_rpkm" label="${tool.name} on ${on_string}: rpkm"/> 89 <data format="tabular" name="out_rpkm" label="${tool.name} on ${on_string}: rpkm"/>
93 <data format="txt" name="out_log" label="${tool.name} on ${on_string}: log"/> 90 <data format="txt" name="out_log" label="${tool.name} on ${on_string}: log"/>
94 </outputs> 91 </outputs>
95 92
96 <help> 93 <help>
120 .. _CRS4 Srl.: http://www.crs4.it/ 117 .. _CRS4 Srl.: http://www.crs4.it/
121 .. _MIT license: http://opensource.org/licenses/MIT 118 .. _MIT license: http://opensource.org/licenses/MIT
122 119
123 If you use this tool in Galaxy, please cite |Cuccuru2013|_. 120 If you use this tool in Galaxy, please cite |Cuccuru2013|_.
124 121
125 .. |Cuccuru2013| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2013) Orione, a web-based framework for NGS analysis in microbiology. *Submitted* 122 .. |Cuccuru2013| 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*, accepted
126 .. _Cuccuru2013: http://orione.crs4.it/ 123 .. _Cuccuru2013: http://orione.crs4.it/
127 124
128 This tool uses `EDGE-pro`_, which is licensed separately. Please cite |Magoc2013|_. 125 This tool uses `EDGE-pro`_, which is licensed separately. Please cite |Magoc2013|_.
129 126
130 .. _EDGE-pro: http://ccb.jhu.edu/software/EDGE-pro/ 127 .. _EDGE-pro: http://ccb.jhu.edu/software/EDGE-pro/