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comparison quantifier.xml @ 0:2c039fc73f1f draft

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author rnateam
date Tue, 27 Jan 2015 09:06:15 -0500
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1 <tool id="rbc_mirdeep2_quantifier" name="MiRDeep2 Quantifier" version="2.0.0">
2 <description>
3 <![CDATA[
4 fast quantitation of reads mapping to known miRBase precursors
5 ]]>
6 </description>
7 <requirements>
8 <requirement type="package" version="2.0">mirdeep2_quantifier</requirement>
9 <requirement type="package" version="0.12.7">bowtie</requirement>
10 <requirement type="package" version="5.18.1">perl</requirement>
11 <requirement type="package" version="1.8.5">vienna_rna</requirement>
12 <requirement type="package" version="2.023">pdf_api2</requirement>
13 </requirements>
14
15 <command>
16 <![CDATA[
17 quantifier.pl
18
19 -p $precursors
20
21 -m $mature
22
23 -r $reads
24
25 #if $species.value != 'all'
26 -t $species
27 #end if
28
29 #if $star_sequences
30 -s $star_sequences
31 #end if
32
33 $sortReadsInPDF
34 $flexibleIdMapping
35 $skipFileConversion
36 $wholePrecursAsMature
37 $discardReadMultiMap
38
39 -e $upstreamNtides
40 -f $downstreamNtides
41 -g $allowedMismatches
42 -y galaxy
43
44 ## html output
45 ;
46 cp expression_galaxy.html $html 2> /dev/null
47
48 ## move pdf directory to be accessible from the new index.html
49 ;
50 mkdir -p $html.files_path 2> /dev/null
51 ;
52 cp -R pdfs_galaxy $html.files_path 2> /dev/null
53
54 ]]>
55 </command>
56 <stdio>
57 <!-- Anything other than zero is an error -->
58 <exit_code range="1:" />
59 <exit_code range=":-1" />
60 <!-- In case the return code has not been set propery check stderr too -->
61 <regex match="Error:" />
62 <regex match="Exception:" />
63 </stdio>
64 <inputs>
65 <param name="reads" format="fasta" type="data" label="Collapsed deep sequencing reads" help="Reads in fasta format. (-r)"/>
66 <param name="precursors" format="fasta" type="data" label="Precursor sequences" help="miRNA precursor sequences from miRBase. (-p)"/>
67 <param name="mature" format="fasta" type="data" label="Mature miRNA sequences" help="Mature miRNA sequences from miRBase. (-m)"/>
68 <param name="species" type="select" label="Search in species" help="If not searching in a specific species all species in your files will be analyzed. (-t)">
69 <option value="all">All species</option>
70 <option value="tni">tetraodon</option>
71 <option value="dps">d.pseudoobscura</option>
72 <option value="dya">d.yakuba</option>
73 <option value="ame">a.mellifera</option>
74 <option value="dmo">d.mojavensis</option>
75 <option value="cel">worm</option>
76 <option value="aga">a.gambiae</option>
77 <option value="cbr">c.briggsae</option>
78 <option value="cin">c.intestinalis</option>
79 <option value="mmu">mouse</option>
80 <option value="xtr">x.tropicalis</option>
81 <option value="eca">horse</option>
82 <option value="cfa">dog</option>
83 <option value="fru">fugu</option>
84 <option value="bta">cow</option>
85 <option value="der">d.erecta</option>
86 <option value="dgr">d.grimshawi</option>
87 <option value="gga">chicken</option>
88 <option value="spu">s.purpuratus</option>
89 <option value="bfl">lancelet</option>
90 <option value="ptr">chimp</option>
91 <option value="dse">d.sechellia</option>
92 <option value="dpe">d.persimilis</option>
93 <option value="dvi">d.virilis</option>
94 <option value="rno">rat</option>
95 <option value="dme">d.melanogaster</option>
96 <option value="lca">cat</option>
97 <option value="sja">c.japonica</option>
98 <option value="dan">d.ananassae</option>
99 <option value="hsa">human</option>
100 <option value="dsi">d.simulans</option>
101 </param>
102 <param name="star_sequences" format="fasta" type="data" optional="true" label="Star sequences" help="From miRBase in fasta format (optional) (-s)"/>
103
104 <!-- <param name="generatePDFs" type="boolean" checked="true" truevalue="" falsevalue="-d" label="Generate PDFs" help="(-d)"/> -->
105 <param name="sortReadsInPDF" type="boolean" checked="true" truevalue="" falsevalue="-o" label="Sort reads by sample in PDF" help="(-o)"/>
106 <param name="flexibleIdMapping" type="boolean" checked="false" truevalue="-k" falsevalue="" label="Include ID-flexible mapping" help="Also considers precursor-mature mappings that have different ids, eg let7c would be allowed to map to pre-let7a. (-k)"/>
107 <param name="skipFileConversion" type="boolean" checked="false" truevalue="-n" falsevalue="" label="Skip file conversion" help="(-n)"/>
108 <param name="skipPrecursMapping" type="boolean" checked="false" truevalue="-x" falsevalue="" label="Skip mapping against precursor" help="(-x)"/>
109 <!-- <param name="noMrdPDF" type="boolean" checked="false" truevalue="-j" falsevalue="" label="Do not create output.mrd file or PDFs" help="(-j)"/> -->
110 <param name="wholePrecursAsMature" type="boolean" checked="false" truevalue="-w" falsevalue="" label="Consider the whole precursor as the 'mature sequence'" help="(-w)"/>
111 <param name="discardReadMultiMap" type="boolean" checked="false" truevalue="-U" falsevalue="" label="Discard all read multimapper" help="(-U)"/>
112
113 <param name="upstreamNtides" type="integer" value="2" minvalue="0" label="Upstream nucleotides" help="Number of nucleotides upstream of the mature sequence to consider. (-e)"/>
114 <param name="downstreamNtides" type="integer" value="5" minvalue="0" label="Downstream nucleotides" help="Number of nucleotides downstream of the mature sequence to consider. (-f)"/>
115 <param name="allowedMismatches" type="integer" value="1" minvalue="0" label="Allowed mismatches" help="Number of allowed mismatches when mapping reads to precursors. (-g)"/>
116 </inputs>
117 <outputs>
118 <data name="miRNAsExpressed" format="tabular" from_work_dir="miRNAs_expressed_all_samples_galaxy.csv" label="output of ${tool.name} on ${on_string}"/>
119 <data format="html" name="html" label="${tool.name} on ${on_string} (html report)"/>
120 </outputs>
121 <tests>
122 <test>
123 <param name="reads" value="reads_collapsed.fa"/>
124 <param name="precursors" value="precursors_ref_this_species.fa"/>
125 <param name="mature" value="mature_ref_this_species.fa"/>
126 <param name="species" value="cel"/>
127 <output name="miRNAsExpressed" file="miRNAs_expressed_all_samples.csv"/>
128 <output name="html" file="expression_galaxy.html"/>
129 </test>
130 </tests>
131 <help>
132 <![CDATA[
133 **What MiRDeep2 Quantifier does**
134
135 The module maps the deep sequencing reads to predefined miRNA precursors and determines by that the expression of the corresponding miRNAs.
136 First, the predefined mature miRNA sequences are mapped to the predefined precursors. Optionally, predefined star sequences can be mapped to the precursors too.
137 By that the mature and star sequence in the precursors are determined. Second, the deep sequencing reads are mapped to the precursors.
138 The number of reads falling into an interval 2nt upstream and 5nt downstream of the mature/star sequence is determined.
139 ]]>
140 </help>
141 <citations>
142 <citation type="doi">10.1093/nar/gkr688</citation>
143 <citation type="doi">10.1002/0471250953.bi1210s36</citation>
144 </citations>
145 </tool>