Mercurial > repos > peterjc > clc_assembly_cell
annotate tools/clc_assembly_cell/clc_assembler.xml @ 4:46a667b5e19e draft
v0.0.6 update optional/required parameters and URLS in docs
author | peterjc |
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date | Wed, 01 Feb 2017 07:05:09 -0500 |
parents | 139b6f0a0bb5 |
children | 31a9169b6222 |
rev | line source |
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46a667b5e19e
v0.0.6 update optional/required parameters and URLS in docs
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1 <tool id="clc_assembler" name="CLC assembler" version="0.0.6"> |
0 | 2 <description>Assembles reads giving a FASTA file</description> |
3 <requirements> | |
4 <requirement type="binary">clc_assembler</requirement> | |
5 </requirements> | |
1 | 6 <stdio> |
7 <!-- Assume anything other than zero is an error --> | |
8 <exit_code range="1:" /> | |
9 <exit_code range=":-1" /> | |
10 </stdio> | |
2 | 11 <version_command>${CLC_ASSEMBLY_CELL:-/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/}clc_assembler | grep -i version</version_command> |
0 | 12 <command>\${CLC_ASSEMBLY_CELL:-/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/}clc_assembler |
13 #for $rg in $read_group | |
14 ##-------------------------------------- | |
15 #if str($rg.segments.type) == "paired" | |
16 -p $rg.segments.placement $rg.segments.dist_mode $rg.segments.min_size $rg.segments.max_size -q -i "$rg.segments.filename1" "$rg.segments.filename2" | |
17 #end if | |
18 ##-------------------------------------- | |
19 #if str($rg.segments.type) == "interleaved" | |
20 -p $rg.segments.placement $rg.segments.dist_mode $rg.segments.min_size $rg.segments.max_size -q "$rg.segments.filename" | |
21 #end if | |
22 ##-------------------------------------- | |
23 #if str($rg.segments.type) == "none" | |
24 -p no -q | |
25 #for $f in $rg.segments.filenames | |
26 "$f" | |
27 #end for | |
28 #end if | |
29 ##-------------------------------------- | |
30 #end for | |
31 -m $min_contig_len | |
32 -o "$out_fasta" | |
33 --cpus \${GALAXY_SLOTS:-4} | |
34 -v | grep -v "^Progress: "</command> | |
35 <inputs> | |
36 <repeat name="read_group" title="Read Group" min="1"> | |
37 <conditional name="segments"> | |
38 <param name="type" type="select" label="Are these paired reads?"> | |
39 <option value="paired">Paired reads (as two files)</option> | |
40 <option value="interleaved">Paired reads (as one interleaved file)</option> | |
41 <option value="none">Unpaired reads (single or orphan reads)</option> | |
42 </param> | |
43 <when value="paired"> | |
44 <param name="placement" type="select" label="Pairing type (segment placing)"> | |
45 <option value="fb">---> <--- (e.g. Sanger capillary or Solexa/Illumina paired-end library)</option> | |
46 <option value="bf"><--- ---> (e.g. Solexa/Illumina mate-pair library)</option> | |
47 <option value="ff">---> ---></option> | |
48 <option value="bb"><--- <---</option> | |
49 </param> | |
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> | |
52 <option value="se">Start to end</option> | |
53 <option value="es">End to start</option> | |
54 <option value="ee">End to end</option> | |
55 </param> | |
56 <!-- TODO - min/max validation done via the <code> tag? --> | |
57 <param name="min_size" type="integer" optional="false" min="0" value="" | |
58 label="Minimum size of 'good' DNA templates in the library preparation" /> | |
59 <param name="max_size" type="integer" optional="false" min="0" value="" | |
60 label="Maximum size of 'good' DNA templates in the library preparation" /> | |
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v0.0.6 update optional/required parameters and URLS in docs
peterjc
parents:
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diff
changeset
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61 <param name="filename1" type="data" format="fastq,fasta" label="Read file one"/> |
46a667b5e19e
v0.0.6 update optional/required parameters and URLS in docs
peterjc
parents:
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diff
changeset
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62 <param name="filename2" type="data" format="fastq,fasta" label="Read file two"/> |
0 | 63 </when> |
64 <when value="interleaved"> | |
65 <param name="placement" type="select" label="Pairing type (segment placing)"> | |
66 <option value="fb">---> <--- (e.g. Sanger capillary or Solexa/Illumina paired-end library)</option> | |
67 <option value="bf"><--- ---> (e.g. Solexa/Illumina mate-pair library)</option> | |
68 <option value="ff">---> ---></option> | |
69 <option value="bb"><-- <--</option> | |
70 </param> | |
71 <param name="dist_mode" type="select" label="How is the fragment distance measured?"> | |
72 <option value="ss">Start to start (e.g. Sanger capillary or Solexa/Illumina libraries)</option> | |
73 <option value="se">Start to end</option> | |
74 <option value="es">End to start</option> | |
75 <option value="ee">End to end</option> | |
76 </param> | |
77 <!-- TODO - min/max validation done via the <code> tag? --> | |
78 <param name="min_size" type="integer" optional="false" min="0" value="" | |
79 label="Minimum size of 'good' DNA templates in the library preparation" /> | |
80 <param name="max_size" type="integer" optional="false" min="0" value="" | |
81 label="Maximum size of 'good' DNA templates in the library preparation" /> | |
4
46a667b5e19e
v0.0.6 update optional/required parameters and URLS in docs
peterjc
parents:
2
diff
changeset
|
82 <param name="filename" type="data" format="fastq,fasta" label="Interleaved read file"/> |
0 | 83 </when> |
84 <when value="none"> | |
4
46a667b5e19e
v0.0.6 update optional/required parameters and URLS in docs
peterjc
parents:
2
diff
changeset
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85 <param name="filenames" type="data" format="fastq,fasta" multiple="true" optional="false" label="Read file(s)" |
0 | 86 help="Multiple files allowed, for example several files of orphan reads." /> |
87 </when> | |
88 </conditional> | |
89 </repeat> | |
90 <param name="min_contig_len" type="integer" optional="false" min="1" value="200" label="Minimum contig length"/> | |
91 <!-- Word size? --> | |
92 <!-- Bubble size? --> | |
93 <!-- Scaffolding options? --> | |
94 <!-- AGP / GFF output? --> | |
95 </inputs> | |
96 <!-- min/max validation? <code file="clc_validator.py" /> --> | |
97 <outputs> | |
98 <data name="out_fasta" format="fasta" label="CLCbio assember contigs (FASTA)" /> | |
99 </outputs> | |
100 <tests> | |
101 <test> | |
102 <param name="read_group_0|segments|type" value="interleaved" /> | |
103 <param name="read_group_0|segments|placement" value="fb" /> | |
104 <param name="read_group_0|segments|dist_mode" value="ss" /> | |
105 <param name="read_group_0|segments|min_size" value="1" /> | |
106 <param name="read_group_0|segments|max_size" value="1000" /> | |
107 <param name="read_group_0|segments|dist_mode" value="ss" /> | |
108 <param name="read_group_0|segments|filename" value="SRR639755_mito_pairs.fastq.gz" ftype="fastqsanger" /> | |
109 <param name="min_contig_len" value="200" /> | |
110 <output name="out_fasta" file="SRR639755_mito_pairs.clc4_de_novo.fasta" ftype="fasta" /> | |
111 </test> | |
112 </tests> | |
113 <help> | |
114 | |
115 **What it does** | |
116 | |
117 Runs the ``clc_assembler`` tool giving a FASTA output file. You would then | |
118 typically map the same set of reads onto this assembly using ``cls_mapper`` | |
119 to any perform downstream analysis using the mapped reads. | |
120 | |
121 | |
122 **Citation** | |
123 | |
124 If you use this Galaxy tool in work leading to a scientific publication please | |
125 cite this wrapper as: | |
126 | |
127 Peter J.A. Cock (2013), Galaxy wrapper for the CLC Assembly Cell suite from CLCbio | |
128 http://toolshed.g2.bx.psu.edu/view/peterjc/clc_assembly_cell | |
129 | |
1 | 130 CLC Assembly Cell, CLC bio (2008--2015) |
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131 https://www.qiagenbioinformatics.com/products/clc-assembly-cell/ |
1 | 132 |
0 | 133 This wrapper is available to install into other Galaxy Instances via the Galaxy |
134 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/clc_assembly_cell | |
135 </help> | |
1 | 136 <citations> |
137 <citation type="bibtex"> | |
138 @MISC{clcbio, | |
139 AUTHOR = {CLC Bio} | |
140 title ={{CLC Assembly Cell}}, | |
4
46a667b5e19e
v0.0.6 update optional/required parameters and URLS in docs
peterjc
parents:
2
diff
changeset
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141 url = {https://www.qiagenbioinformatics.com/products/clc-assembly-cell/}, |
1 | 142 year = {2008--2015} |
143 } | |
144 </citation> | |
145 </citations> | |
0 | 146 </tool> |