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