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comparison tools/clc_assembly_cell/clc_assembler.xml @ 0:7b96d8a3262f draft

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Uploaded v0.0.0, wrappers for the CLCbio assember and mapper only.
author peterjc
date Thu, 31 Oct 2013 07:57:41 -0400
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children 6e145e4715a7
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1 <tool id="clc_assembler" name="CLC assembler" version="0.0.1">
2 <description>Assembles reads giving a FASTA file</description>
3 <requirements>
4 <requirement type="binary">clc_assembler</requirement>
5 </requirements>
6 <version_command>/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
8 #for $rg in $read_group
9 ##--------------------------------------
10 #if str($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" "$rg.segments.filename2"
12 #end if
13 ##--------------------------------------
14 #if str($rg.segments.type) == "interleaved"
15 -p $rg.segments.placement $rg.segments.dist_mode $rg.segments.min_size $rg.segments.max_size -q "$rg.segments.filename"
16 #end if
17 ##--------------------------------------
18 #if str($rg.segments.type) == "none"
19 -p no -q
20 #for $f in $rg.segments.filenames
21 "$f"
22 #end for
23 #end if
24 ##--------------------------------------
25 #end for
26 -o "$out_fasta"
27 --cpus \$GALAXY_SLOTS
28 -v | grep -v "^Progress: "</command>
29 <stdio>
30 <!-- Assume anything other than zero is an error -->
31 <exit_code range="1:" />
32 <exit_code range=":-1" />
33 </stdio>
34 <inputs>
35 <repeat name="read_group" title="Read Group" min="1">
36 <conditional name="segments">
37 <param name="type" type="select" label="Are these paired reads?">
38 <option value="paired">Paired reads (as two files)</option>
39 <option value="interleaved">Paired reads (as one interleaved file)</option>
40 <option value="none">Unpaired reads (single or orphan reads)</option>
41 </param>
42 <when value="paired">
43 <param name="placement" type="select" label="Pairing type (segment placing)">
44 <option value="fb">---&gt; &lt;--- (e.g. Sanger capillary or Solexa/Illumina paired-end library)</option>
45 <option value="bf">&lt;--- ---&gt; (e.g. Solexa/Illumina mate-pair library)</option>
46 <option value="ff">---&gt; ---&gt;</option>
47 <option value="bb">&lt;--- &lt;---</option>
48 </param>
49 <param name="dist_mode" type="select" label="How is the fragment distance measured?">
50 <option value="ss">Start to start (e.g. Sanger capillary or Solexa/Illumina libraries)</option>
51 <option value="se">Start to end</option>
52 <option value="es">End to start</option>
53 <option value="ee">End to end</option>
54 </param>
55 <!-- TODO - min/max validation done via the <code> tag? -->
56 <param name="min_size" type="integer" optional="false" min="0" value=""
57 label="Minimum size of 'good' DNA templates in the library preparation" />
58 <param name="max_size" type="integer" optional="false" min="0" value=""
59 label="Maximum size of 'good' DNA templates in the library preparation" />
60 <param name="filename1" type="data" format="fastq,fasta" required="true" label="Read file one"/>
61 <param name="filename2" type="data" format="fastq,fasta" required="true" label="Read file two"/>
62 </when>
63 <when value="interleaved">
64 <param name="placement" type="select" label="Pairing type (segment placing)">
65 <option value="fb">---&gt; &lt;--- (e.g. Sanger capillary or Solexa/Illumina paired-end library)</option>
66 <option value="bf">&lt;--- ---&gt; (e.g. Solexa/Illumina mate-pair library)</option>
67 <option value="ff">---&gt; ---&gt;</option>
68 <option value="bb">&lt;-- &lt;--</option>
69 </param>
70 <param name="dist_mode" type="select" label="How is the fragment distance measured?">
71 <option value="ss">Start to start (e.g. Sanger capillary or Solexa/Illumina libraries)</option>
72 <option value="se">Start to end</option>
73 <option value="es">End to start</option>
74 <option value="ee">End to end</option>
75 </param>
76 <!-- TODO - min/max validation done via the <code> tag? -->
77 <param name="min_size" type="integer" optional="false" min="0" value=""
78 label="Minimum size of 'good' DNA templates in the library preparation" />
79 <param name="max_size" type="integer" optional="false" min="0" value=""
80 label="Maximum size of 'good' DNA templates in the library preparation" />
81 <param name="filename" type="data" format="fastq,fasta" required="true" label="Interleaved read file"/>
82 </when>
83 <when value="none">
84 <param name="filenames" type="data" format="fastq,fasta" multiple="true" required="true" label="Read file(s)"
85 help="Multiple files allowed, for example several files of orphan reads." />
86 </when>
87 </conditional>
88 </repeat>
89 <!-- Word size? -->
90 <!-- Bubble size? -->
91 <!-- Scaffolding options? -->
92 <!-- Minimum contig length? -->
93 <!-- AGP / GFF output? -->
94 </inputs>
95 <!-- min/max validation? <code file="clc_validator.py" /> -->
96 <outputs>
97 <data name="out_fasta" format="fasta" label="CLCbio assember contigs (FASTA)" />
98 </outputs>
99 <tests>
100 <!-- TODO -->
101 </tests>
102 <help>
103
104 **What it does**
105
106 Runs the ``clc_assembler`` tool giving a FASTA output file. You would then
107 typically map the same set of reads onto this assembly using ``cls_mapper``
108 to any perform downstream analysis using the mapped reads.
109
110
111 **Citation**
112
113 If you use this Galaxy tool in work leading to a scientific publication please
114 cite this wrapper as:
115
116 Peter J.A. Cock (2013), Galaxy wrapper for the CLC Assembly Cell suite from CLCbio
117 http://toolshed.g2.bx.psu.edu/view/peterjc/clc_assembly_cell
118
119 This wrapper is available to install into other Galaxy Instances via the Galaxy
120 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/clc_assembly_cell
121 </help>
122 </tool>