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comparison edge_pro.xml @ 4:d5464c9e1723 draft

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Add support for paired collection of FASTQ (thanks to Inge Alexander Raknes).
author crs4
date Tue, 17 Mar 2015 10:44:33 -0400
parents ddcbf8732706
children e6e6f5f9b9c4
comparison
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3:ddcbf8732706 4:d5464c9e1723
8 edge.pl -t \${GALAXY_SLOTS:-4} -o edge_out 8 edge.pl -t \${GALAXY_SLOTS:-4} -o edge_out
9 ## Mandatory input parameters 9 ## Mandatory input parameters
10 -g $genome 10 -g $genome
11 -p $ptt 11 -p $ptt
12 -r $rnt 12 -r $rnt
13 ## First input file always required 13
14 -u $singlePaired.input1 14 #if $singlePaired.sPaired == "single"
15 ## Second input only if input is paired-end 15 -u $singlePaired.input1
16 #if $singlePaired.sPaired == "paired" 16 #else if $singlePaired.sPaired == "paired"
17 -u $singlePaired.input1
17 -v $singlePaired.input2 18 -v $singlePaired.input2
19 #else if $singlePaired.sPaired == "pairedCollection"
20 -u $singlePaired.input.forward
21 -v $singlePaired.input.reverse
22 #end if
23
24 #if $singlePaired.sPaired in ["paired", "pairedCollection"]
18 #if str($singlePaired.minInsertSize) 25 #if str($singlePaired.minInsertSize)
19 -m $singlePaired.minInsertSize 26 -m $singlePaired.minInsertSize
20 #end if 27 #end if
21 #if str($singlePaired.maxInsertSize) 28 #if str($singlePaired.maxInsertSize)
22 -M $singlePaired.maxInsertSize 29 -M $singlePaired.maxInsertSize
50 <inputs> 57 <inputs>
51 <conditional name="singlePaired"> 58 <conditional name="singlePaired">
52 <param name="sPaired" type="select" label="Is this library mate-paired?"> 59 <param name="sPaired" type="select" label="Is this library mate-paired?">
53 <option value="single">Single-end</option> 60 <option value="single">Single-end</option>
54 <option value="paired">Paired-end</option> 61 <option value="paired">Paired-end</option>
62 <option value="pairedCollection">Paired-end collection</option>
55 </param> 63 </param>
56 <when value="single"> 64 <when value="single">
57 <param format="fastqsanger" name="input1" type="data" label="FASTQ file" help="FASTQ format with Sanger-scaled quality values (Galaxy fastqsanger datatype)"/> 65 <param format="fastqsanger" name="input1" type="data" label="FASTQ file" help="FASTQ format with Sanger-scaled quality values (Galaxy fastqsanger datatype)"/>
58 </when> 66 </when>
59 <when value="paired"> 67 <when value="paired">
60 <param format="fastqsanger" name="input1" type="data" label="Forward FASTQ file" help="FASTQ format with Sanger-scaled quality values (Galaxy fastqsanger datatype)" /> 68 <param format="fastqsanger" name="input1" type="data" label="Forward 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)" /> 69 <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)" /> 70 <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)" /> 71 <param name="maxInsertSize" type="integer" optional="true" min="1" value="500" label="Maximun insert size in paired-end library for Bowtie2 (-M)" />
72 </when>
73 <when value="pairedCollection">
74 <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)" />
75 <param name="minInsertSize" type="integer" optional="true" min="0" value="0" label="Minimun insert size in paired-end library for Bowtie2 (-m)" />
76 <param name="maxInsertSize" type="integer" optional="true" min="1" value="500" label="Maximun insert size in paired-end library for Bowtie2 (-M)" />
64 </when> 77 </when>
65 </conditional> 78 </conditional>
66 79
67 <param format="fasta" name="genome" type="data" label="Select the reference genome from your history (-g)" help="FASTA format" /> 80 <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)" /> 81 <param format="ptt" name="ptt" type="data" label="Coordinates of coding genes (PTT file)" help="PTT file with coordinates of coding genes (-p)" />