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comparison pear.xml @ 7:5bbdf641a2d5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pear commit baa6a1ec8b3c440cdf73409ccaafcd303e9f4e72
author iuc
date Mon, 30 Nov 2015 21:59:45 -0500
parents 2f6e6d74144e
children bb0164f44f3c
comparison
equal deleted inserted replaced
6:5e0bd8204933 7:5bbdf641a2d5
1 <tool id="iuc_pear" name="Pear" version="0.9.6.0"> 1 <tool id="iuc_pear" name="Pear" version="0.9.6.1">
2 <description>Paired-End read merger</description> 2 <description>Paired-End read merger</description>
3 <!--<version_command>bismark version</version_command>-->
4 <requirements> 3 <requirements>
5 <requirement type="package" version="0.9.6">pear</requirement> 4 <requirement type="package" version="0.9.6">pear</requirement>
6 </requirements> 5 </requirements>
7 <stdio> 6 <stdio>
8 <exit_code range="1:" /> 7 <exit_code range="1:" />
14 <![CDATA[ 13 <![CDATA[
15 pear 14 pear
16 #if str( $library.type ) == "paired": 15 #if str( $library.type ) == "paired":
17 -f "$library.forward" 16 -f "$library.forward"
18 -r "$library.reverse" 17 -r "$library.reverse"
18 #if $library.forward.is_of_type( 'fastqillumina' ):
19 --phred-base 64
20 #else:
21 --phred-base 33
22 #end if
19 #else 23 #else
20 ## prepare collection 24 ## prepare collection
21 -f $library.input_collection.forward 25 -f $library.input_collection.forward
22 -r $library.input_collection.reverse 26 -r $library.input_collection.reverse
27 #if $library.input_collection.forward.is_of_type( 'fastqillumina' ):
28 --phred-base 64
29 #else:
30 --phred-base 33
31 #end if
23 #end if 32 #end if
24 33
25 --output pear 34 --output pear
26 --p-value $pvalue 35 --p-value $pvalue
27 --min-overlap $min_overlap 36 --min-overlap $min_overlap
45 <param name="type" type="select" label="Dataset type"> 54 <param name="type" type="select" label="Dataset type">
46 <option value="paired">Paired-end</option> 55 <option value="paired">Paired-end</option>
47 <option value="paired_collection">Paired-end Dataset Collection</option> 56 <option value="paired_collection">Paired-end Dataset Collection</option>
48 </param> 57 </param>
49 <when value="paired"> 58 <when value="paired">
50 <param name="forward" type="data" format="fastqillumina, fastqsanger, fastq" 59 <param name="forward" type="data" format="fastqillumina,fastqsanger"
51 label="Name of file that contains the forward paired-end reads" help="-f" /> 60 label="Name of file that contains the forward paired-end reads" help="-f" />
52 <param name="reverse" type="data" format="fastqillumina, fastqsanger, fastq" 61 <param name="reverse" type="data" format="fastqillumina,fastqsanger"
53 label="Name of file that contains the reverse paired-end reads" help="-r" /> 62 label="Name of file that contains the reverse paired-end reads" help="-r" />
54 </when> 63 </when>
55 <when value="paired_collection"> 64 <when value="paired_collection">
56 <param name="input_collection" format="fastqillumina, fastqsanger, fastq" 65 <param name="input_collection" format="fastqillumina,fastqsanger"
57 type="data_collection" collection_type="paired" 66 type="data_collection" collection_type="paired"
58 label="FASTQ Paired Dataset" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33. (-f and -r)" /> 67 label="FASTQ Paired Dataset" help="Nucleotide-space: Must have PHRED-scaled quality values. (-f and -r)" />
59 </when> 68 </when>
60 </conditional> 69 </conditional>
61 70
62 <!-- optional --> 71 <!-- optional -->
63 <param name="pvalue" type="float" value="0.01" min="0" optional="True" max="1" label="Specify a p-value for the statistical test" 72 <param name="pvalue" type="float" value="0.01" min="0" optional="True" max="1" label="Specify a p-value for the statistical test"
106 <option value="reverse">Reverse unassembled reads</option> 115 <option value="reverse">Reverse unassembled reads</option>
107 <option value="discarded">Discarded reads</option> 116 <option value="discarded">Discarded reads</option>
108 </param> 117 </param>
109 </inputs> 118 </inputs>
110 <outputs> 119 <outputs>
111 <data format="fastq" name="assembled_reads" from_work_dir="pear.assembled.fastq" label="${tool.name} on ${on_string}: Assembled reads"> 120 <data format="input" name="assembled_reads" from_work_dir="pear.assembled.fastq" label="${tool.name} on ${on_string}: Assembled reads">
112 <filter>'assembled' in outputs</filter> 121 <filter>'assembled' in outputs</filter>
113 </data> 122 </data>
114 <data format="fastq" name="unassembled_forward_reads" from_work_dir="pear.unassembled.forward.fastq" label="${tool.name} on ${on_string}: Unassembled forward reads"> 123 <data format="input" name="unassembled_forward_reads" from_work_dir="pear.unassembled.forward.fastq" label="${tool.name} on ${on_string}: Unassembled forward reads">
115 <filter>'forward' in outputs</filter> 124 <filter>'forward' in outputs</filter>
116 </data> 125 </data>
117 <data format="fastq" name="unassembled_reverse_reads" from_work_dir="pear.unassembled.reverse.fastq" label="${tool.name} on ${on_string}: Unassembled reverse reads"> 126 <data format="input" name="unassembled_reverse_reads" from_work_dir="pear.unassembled.reverse.fastq" label="${tool.name} on ${on_string}: Unassembled reverse reads">
118 <filter>'reverse' in outputs</filter> 127 <filter>'reverse' in outputs</filter>
119 </data> 128 </data>
120 <data format="fastq" name="discarded_reads" from_work_dir="pear.discarded.fastq" label="${tool.name} on ${on_string}: Discarded reads"> 129 <data format="input" name="discarded_reads" from_work_dir="pear.discarded.fastq" label="${tool.name} on ${on_string}: Discarded reads">
121 <filter>'discarded' in outputs</filter> 130 <filter>'discarded' in outputs</filter>
122 </data> 131 </data>
123 </outputs> 132 </outputs>
124 <tests> 133 <tests>
125 <test> 134 <test>
126 <param name="forward" value="forward.fastq" ftype="fastq" /> 135 <param name="forward" value="forward.fastq" ftype="fastqsanger" />
127 <param name="reverse" value="reverse.fastq" ftype="fastq" /> 136 <param name="reverse" value="reverse.fastq" ftype="fastqsanger" />
128 <param name="min_overlap" value="10" /> 137 <param name="min_overlap" value="10" />
129 <param name="min_assembly_length" value="50" /> 138 <param name="min_assembly_length" value="50" />
130 <param name="cap" value="0" /> 139 <param name="cap" value="0" />
131 <param name="outputs" value="assembled,forward" /> 140 <param name="outputs" value="assembled,forward" />
132 <output name="assembled_reads" file="pear_assembled_results1.fastq" ftype="fastq"/> 141 <output name="assembled_reads" file="pear_assembled_results1.fastq" ftype="fastqsanger"/>
133 <output name="unassembled_forward_reads" file="pear_unassembled_forward_results1.fastq" ftype="fastq"/> 142 <output name="unassembled_forward_reads" file="pear_unassembled_forward_results1.fastq" ftype="fastqsanger"/>
134 </test> 143 </test>
135 </tests> 144 </tests>
136 <help> 145 <help>
137 <![CDATA[ 146 <![CDATA[
138 147