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comparison tools/clc_assembly_cell/clc_assembler.xml @ 3:93ef6468b288 draft

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Uploaded v0.0.2 which uses the described environment variable to find the binaries
author peterjc
date Fri, 21 Nov 2014 06:40:45 -0500
parents 6e145e4715a7
children 95a5f56a24eb
comparison
equal deleted inserted replaced
2:6e145e4715a7 3:93ef6468b288
1 <tool id="clc_assembler" name="CLC assembler" version="0.0.1"> 1 <tool id="clc_assembler" name="CLC assembler" version="0.0.2">
2 <description>Assembles reads giving a FASTA file</description> 2 <description>Assembles reads giving a FASTA file</description>
3 <requirements> 3 <requirements>
4 <requirement type="binary">clc_assembler</requirement> 4 <requirement type="binary">clc_assembler</requirement>
5 </requirements> 5 </requirements>
6 <version_command>/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/clc_assembler | grep -i version</version_command> 6 <version_command>\${CLC_ASSEMBLY_CELL:-/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/}clc_assembler | grep -i version</version_command>
7 <command>/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/clc_assembler 7 <command>\${CLC_ASSEMBLY_CELL:-/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/}clc_assembler
8 #for $rg in $read_group 8 #for $rg in $read_group
9 ##-------------------------------------- 9 ##--------------------------------------
10 #if str($rg.segments.type) == "paired" 10 #if str($rg.segments.type) == "paired"
11 -p $rg.segments.placement $rg.segments.dist_mode $rg.segments.min_size $rg.segments.max_size -q -i "$rg.segments.filename1" "$rg.segments.filename2" 11 -p $rg.segments.placement $rg.segments.dist_mode $rg.segments.min_size $rg.segments.max_size -q -i "$rg.segments.filename1" "$rg.segments.filename2"
12 #end if 12 #end if
23 #end if 23 #end if
24 ##-------------------------------------- 24 ##--------------------------------------
25 #end for 25 #end for
26 -m $min_contig_len 26 -m $min_contig_len
27 -o "$out_fasta" 27 -o "$out_fasta"
28 --cpus \$GALAXY_SLOTS 28 --cpus \${GALAXY_SLOTS:-4}
29 -v | grep -v "^Progress: "</command> 29 -v | grep -v "^Progress: "</command>
30 <stdio> 30 <stdio>
31 <!-- Assume anything other than zero is an error --> 31 <!-- Assume anything other than zero is an error -->
32 <exit_code range="1:" /> 32 <exit_code range="1:" />
33 <exit_code range=":-1" /> 33 <exit_code range=":-1" />
35 <inputs> 35 <inputs>
36 <repeat name="read_group" title="Read Group" min="1"> 36 <repeat name="read_group" title="Read Group" min="1">
37 <conditional name="segments"> 37 <conditional name="segments">
38 <param name="type" type="select" label="Are these paired reads?"> 38 <param name="type" type="select" label="Are these paired reads?">
39 <option value="paired">Paired reads (as two files)</option> 39 <option value="paired">Paired reads (as two files)</option>
40 <option value="interleaved">Paired reads (as one interleaved file)</option> 40 <option value="interleaved">Paired reads (as one interleaved file)</option>
41 <option value="none">Unpaired reads (single or orphan reads)</option> 41 <option value="none">Unpaired reads (single or orphan reads)</option>
42 </param> 42 </param>
43 <when value="paired"> 43 <when value="paired">
44 <param name="placement" type="select" label="Pairing type (segment placing)"> 44 <param name="placement" type="select" label="Pairing type (segment placing)">
45 <option value="fb">---&gt; &lt;--- (e.g. Sanger capillary or Solexa/Illumina paired-end library)</option> 45 <option value="fb">---&gt; &lt;--- (e.g. Sanger capillary or Solexa/Illumina paired-end library)</option>
46 <option value="bf">&lt;--- ---&gt; (e.g. Solexa/Illumina mate-pair library)</option> 46 <option value="bf">&lt;--- ---&gt; (e.g. Solexa/Illumina mate-pair library)</option>
47 <option value="ff">---&gt; ---&gt;</option> 47 <option value="ff">---&gt; ---&gt;</option>
48 <option value="bb">&lt;--- &lt;---</option> 48 <option value="bb">&lt;--- &lt;---</option>
49 </param> 49 </param>
50 <param name="dist_mode" type="select" label="How is the fragment distance measured?"> 50 <param name="dist_mode" type="select" label="How is the fragment distance measured?">
51 <option value="ss">Start to start (e.g. Sanger capillary or Solexa/Illumina libraries)</option> 51 <option value="ss">Start to start (e.g. Sanger capillary or Solexa/Illumina libraries)</option>
52 <option value="se">Start to end</option> 52 <option value="se">Start to end</option>
53 <option value="es">End to start</option> 53 <option value="es">End to start</option>
54 <option value="ee">End to end</option> 54 <option value="ee">End to end</option>
55 </param> 55 </param>
56 <!-- TODO - min/max validation done via the <code> tag? --> 56 <!-- TODO - min/max validation done via the <code> tag? -->
57 <param name="min_size" type="integer" optional="false" min="0" value="" 57 <param name="min_size" type="integer" optional="false" min="0" value=""
58 label="Minimum size of 'good' DNA templates in the library preparation" /> 58 label="Minimum size of 'good' DNA templates in the library preparation" />
59 <param name="max_size" type="integer" optional="false" min="0" value="" 59 <param name="max_size" type="integer" optional="false" min="0" value=""
60 label="Maximum size of 'good' DNA templates in the library preparation" /> 60 label="Maximum size of 'good' DNA templates in the library preparation" />
61 <param name="filename1" type="data" format="fastq,fasta" required="true" label="Read file one"/> 61 <param name="filename1" type="data" format="fastq,fasta" required="true" label="Read file one"/>
62 <param name="filename2" type="data" format="fastq,fasta" required="true" label="Read file two"/> 62 <param name="filename2" type="data" format="fastq,fasta" required="true" label="Read file two"/>
63 </when> 63 </when>
64 <when value="interleaved"> 64 <when value="interleaved">
65 <param name="placement" type="select" label="Pairing type (segment placing)"> 65 <param name="placement" type="select" label="Pairing type (segment placing)">
66 <option value="fb">---&gt; &lt;--- (e.g. Sanger capillary or Solexa/Illumina paired-end library)</option> 66 <option value="fb">---&gt; &lt;--- (e.g. Sanger capillary or Solexa/Illumina paired-end library)</option>
82 <param name="filename" type="data" format="fastq,fasta" required="true" label="Interleaved read file"/> 82 <param name="filename" type="data" format="fastq,fasta" required="true" label="Interleaved read file"/>
83 </when> 83 </when>
84 <when value="none"> 84 <when value="none">
85 <param name="filenames" type="data" format="fastq,fasta" multiple="true" required="true" label="Read file(s)" 85 <param name="filenames" type="data" format="fastq,fasta" multiple="true" required="true" label="Read file(s)"
86 help="Multiple files allowed, for example several files of orphan reads." /> 86 help="Multiple files allowed, for example several files of orphan reads." />
87 </when> 87 </when>
88 </conditional> 88 </conditional>
89 </repeat> 89 </repeat>
90 <param name="min_contig_len" type="integer" optional="false" min="1" value="200" label="Minimum contig length"/> 90 <param name="min_contig_len" type="integer" optional="false" min="1" value="200" label="Minimum contig length"/>
91 <!-- Word size? --> 91 <!-- Word size? -->
92 <!-- Bubble size? --> 92 <!-- Bubble size? -->
93 <!-- Scaffolding options? --> 93 <!-- Scaffolding options? -->
94 <!-- AGP / GFF output? --> 94 <!-- AGP / GFF output? -->
95 </inputs> 95 </inputs>
96 <!-- min/max validation? <code file="clc_validator.py" /> --> 96 <!-- min/max validation? <code file="clc_validator.py" /> -->
97 <outputs> 97 <outputs>
98 <data name="out_fasta" format="fasta" label="CLCbio assember contigs (FASTA)" /> 98 <data name="out_fasta" format="fasta" label="CLCbio assember contigs (FASTA)" />
99 </outputs> 99 </outputs>
100 <tests> 100 <tests>
101 <!-- Review this test once Galaxy handles repeat groups better
102 <test> 101 <test>
103 <param name="type" value="interleaved" /> 102 <param name="read_group_0|segments|type" value="interleaved" />
104 <param name="placement" value="fb" /> 103 <param name="read_group_0|segments|placement" value="fb" />
105 <param name="dist_mode" value="ss" /> 104 <param name="read_group_0|segments|dist_mode" value="ss" />
106 <param name="min_size" value="1" /> 105 <param name="read_group_0|segments|min_size" value="1" />
107 <param name="max_size" value="1000" /> 106 <param name="read_group_0|segments|max_size" value="1000" />
108 <param name="dist_mode" value="ss" /> 107 <param name="read_group_0|segments|dist_mode" value="ss" />
109 <param name="filename" value="SRR639755_mito_pairs.fastq.gz" ftype="fastqsanger" /> 108 <param name="read_group_0|segments|filename" value="SRR639755_mito_pairs.fastq.gz" ftype="fastqsanger" />
110 <param name="min_contig_len" value="200" /> 109 <param name="min_contig_len" value="200" />
111 <output name="out_fasta" file="SRR639755_mito_pairs.clc4_de_novo.fasta" ftype="fasta" /> 110 <output name="out_fasta" file="SRR639755_mito_pairs.clc4_de_novo.fasta" ftype="fasta" />
112 </test> 111 </test>
113 -->
114 </tests> 112 </tests>
115 <help> 113 <help>
116 114
117 **What it does** 115 **What it does**
118 116