annotate quantifier.xml @ 1:40dc77f3730c draft

Uploaded
author rnateam
date Wed, 04 Feb 2015 12:45:52 -0500
parents 2c039fc73f1f
children d5ea61ff12eb
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
1 <tool id="rbc_mirdeep2_quantifier" name="MiRDeep2 Quantifier" version="2.0.0">
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
2 <description>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
3 <![CDATA[
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
4 fast quantitation of reads mapping to known miRBase precursors
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
5 ]]>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
6 </description>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
7 <requirements>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
8 <requirement type="package" version="2.0">mirdeep2_quantifier</requirement>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
9 <requirement type="package" version="0.12.7">bowtie</requirement>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
10 <requirement type="package" version="5.18.1">perl</requirement>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
11 <requirement type="package" version="1.8.5">vienna_rna</requirement>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
12 <requirement type="package" version="2.023">pdf_api2</requirement>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
13 </requirements>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
14
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
15 <command>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
16 <![CDATA[
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
17 quantifier.pl
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
18
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
19 -p $precursors
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
20
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
21 -m $mature
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
22
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
23 -r $reads
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
24
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
25 #if $species.value != 'all'
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
26 -t $species
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
27 #end if
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
28
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
29 #if $star_sequences
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
30 -s $star_sequences
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
31 #end if
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
32
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
33 $sortReadsInPDF
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
34 $flexibleIdMapping
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
35 $skipFileConversion
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
36 $wholePrecursAsMature
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
37 $discardReadMultiMap
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
38
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
39 -e $upstreamNtides
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
40 -f $downstreamNtides
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
41 -g $allowedMismatches
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
42 -y galaxy
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
43
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
44 ## html output
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
45 ;
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
46 cp expression_galaxy.html $html 2> /dev/null
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
47
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
48 ## move pdf directory to be accessible from the new index.html
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
49 ;
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
50 mkdir -p $html.files_path 2> /dev/null
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
51 ;
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
52 cp -R pdfs_galaxy $html.files_path 2> /dev/null
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
53
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
54 ]]>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
55 </command>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
56 <stdio>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
57 <!-- Anything other than zero is an error -->
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
58 <exit_code range="1:" />
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
59 <exit_code range=":-1" />
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
60 <!-- In case the return code has not been set propery check stderr too -->
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
61 <regex match="Error:" />
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
62 <regex match="Exception:" />
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
63 </stdio>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
64 <inputs>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
65 <param name="reads" format="fasta" type="data" label="Collapsed deep sequencing reads" help="Reads in fasta format. (-r)"/>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
66 <param name="precursors" format="fasta" type="data" label="Precursor sequences" help="miRNA precursor sequences from miRBase. (-p)"/>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
67 <param name="mature" format="fasta" type="data" label="Mature miRNA sequences" help="Mature miRNA sequences from miRBase. (-m)"/>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
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)">
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
69 <option value="all">All species</option>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
70 <option value="tni">tetraodon</option>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
71 <option value="dps">d.pseudoobscura</option>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
72 <option value="dya">d.yakuba</option>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
73 <option value="ame">a.mellifera</option>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
74 <option value="dmo">d.mojavensis</option>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
75 <option value="cel">worm</option>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
76 <option value="aga">a.gambiae</option>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
77 <option value="cbr">c.briggsae</option>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
78 <option value="cin">c.intestinalis</option>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
79 <option value="mmu">mouse</option>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
80 <option value="xtr">x.tropicalis</option>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
81 <option value="eca">horse</option>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
82 <option value="cfa">dog</option>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
83 <option value="fru">fugu</option>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
84 <option value="bta">cow</option>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
85 <option value="der">d.erecta</option>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
86 <option value="dgr">d.grimshawi</option>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
87 <option value="gga">chicken</option>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
88 <option value="spu">s.purpuratus</option>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
89 <option value="bfl">lancelet</option>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
90 <option value="ptr">chimp</option>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
91 <option value="dse">d.sechellia</option>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
92 <option value="dpe">d.persimilis</option>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
93 <option value="dvi">d.virilis</option>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
94 <option value="rno">rat</option>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
95 <option value="dme">d.melanogaster</option>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
96 <option value="lca">cat</option>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
97 <option value="sja">c.japonica</option>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
98 <option value="dan">d.ananassae</option>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
99 <option value="hsa">human</option>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
100 <option value="dsi">d.simulans</option>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
101 </param>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
102 <param name="star_sequences" format="fasta" type="data" optional="true" label="Star sequences" help="From miRBase in fasta format (optional) (-s)"/>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
103
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
104 <!-- <param name="generatePDFs" type="boolean" checked="true" truevalue="" falsevalue="-d" label="Generate PDFs" help="(-d)"/> -->
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
105 <param name="sortReadsInPDF" type="boolean" checked="true" truevalue="" falsevalue="-o" label="Sort reads by sample in PDF" help="(-o)"/>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
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)"/>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
107 <param name="skipFileConversion" type="boolean" checked="false" truevalue="-n" falsevalue="" label="Skip file conversion" help="(-n)"/>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
108 <param name="skipPrecursMapping" type="boolean" checked="false" truevalue="-x" falsevalue="" label="Skip mapping against precursor" help="(-x)"/>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
109 <!-- <param name="noMrdPDF" type="boolean" checked="false" truevalue="-j" falsevalue="" label="Do not create output.mrd file or PDFs" help="(-j)"/> -->
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
110 <param name="wholePrecursAsMature" type="boolean" checked="false" truevalue="-w" falsevalue="" label="Consider the whole precursor as the 'mature sequence'" help="(-w)"/>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
111 <param name="discardReadMultiMap" type="boolean" checked="false" truevalue="-U" falsevalue="" label="Discard all read multimapper" help="(-U)"/>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
112
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
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)"/>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
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)"/>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
115 <param name="allowedMismatches" type="integer" value="1" minvalue="0" label="Allowed mismatches" help="Number of allowed mismatches when mapping reads to precursors. (-g)"/>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
116 </inputs>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
117 <outputs>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
118 <data name="miRNAsExpressed" format="tabular" from_work_dir="miRNAs_expressed_all_samples_galaxy.csv" label="output of ${tool.name} on ${on_string}"/>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
119 <data format="html" name="html" label="${tool.name} on ${on_string} (html report)"/>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
120 </outputs>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
121 <tests>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
122 <test>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
123 <param name="reads" value="reads_collapsed.fa"/>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
124 <param name="precursors" value="precursors_ref_this_species.fa"/>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
125 <param name="mature" value="mature_ref_this_species.fa"/>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
126 <param name="species" value="cel"/>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
127 <output name="miRNAsExpressed" file="miRNAs_expressed_all_samples.csv"/>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
128 <output name="html" file="expression_galaxy.html"/>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
129 </test>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
130 </tests>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
131 <help>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
132 <![CDATA[
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
133 **What MiRDeep2 Quantifier does**
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
134
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
135 The module maps the deep sequencing reads to predefined miRNA precursors and determines by that the expression of the corresponding miRNAs.
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
136 First, the predefined mature miRNA sequences are mapped to the predefined precursors. Optionally, predefined star sequences can be mapped to the precursors too.
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
137 By that the mature and star sequence in the precursors are determined. Second, the deep sequencing reads are mapped to the precursors.
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
138 The number of reads falling into an interval 2nt upstream and 5nt downstream of the mature/star sequence is determined.
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
139 ]]>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
140 </help>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
141 <citations>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
142 <citation type="doi">10.1093/nar/gkr688</citation>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
143 <citation type="doi">10.1002/0471250953.bi1210s36</citation>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
144 </citations>
2c039fc73f1f Imported from capsule None
rnateam
parents:
diff changeset
145 </tool>