annotate siRNA.xml @ 52:8b8c356e6db5 draft

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author big-tiandm
date Fri, 05 Dec 2014 01:28:46 -0500
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1 <tool id="plant_sirna_v1" name="siRNA" veision="1.0.0">
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2 <description>tool for plant siRNA analisis</description>
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3
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4 <requirements>
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5 <requirement type="set_environment">SCRIPT_PATH</requirement>
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6 <requirement type="package" version="0.12.7">bowtie</requirement>
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7 <requirement type="package" version="3.0.1">R</requirement>
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8 <requirement type="package" version="0.0.13">fastx_toolkit </requirement>
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9 <requirement type="package" version="1.96">threads</requirement>
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10 <requirement type="package" version="1.06">Parallel-ForkManager</requirement>
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11 <requirement type="package" version="2.59">SVG</requirement>
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12 <requirement type="package" version="1.4_001">Boost-Graph</requirement>
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13 </requirements>
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14
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15 <command interpreter="perl">siRNA_pipeline.pl
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16 ## Change this to accommodate the number of threads you have available.
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17 -t \${GALAXY_SLOTS:-4}
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18
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19 -path \$SCRIPT_PATH
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20
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21 ## prepare bowtie index
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22 #set index_path = ''
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23 #if str($reference_genome.source) == "history":
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24 bowtie-build "$reference_genome.own_file" genome; ln -s "$reference_genome.own_file" genome.fa;
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25 #set index_path = 'genome'
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26 #else:
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27 #set index_path = $reference_genome.index.fields.path
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28 #end if
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29
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30
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31 ## Do or not annotate siRNAs by function
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32 #if $params.function_anno == "yes":
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33 -nat $params.nat -repeat $params.repeat
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34 #end if
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35
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36 ## Do or not DEG
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37 #if $degseq.degseq_analysis == "yes" :
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38 -deg $degseq.deg
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39 #end if
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40
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41 -i $reads -config $config -n $hits -format $format -g ${index_path}.fa -idx $index_path -f $gff -mis $mis -d $d -p $p -l $l -cen $cen -span $span > run.log
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42
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43 </command>
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44
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45 <inputs>
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46
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47 <param name="config" type="data" label="Raw data configs file" />
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48 <param name="reads" type="data" label="Input Fasta. file of candidate microRNA sequence" />
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49
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50 <param name="format" type="select" lable=" data format" multiple="false">
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51 <option value="fastq">Raw data is fastq. format</option>
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52 <option value="fasta">Raw data is fasta. format</option>
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53 </param>
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54
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55
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56 <conditional name="reference_genome">
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57 <param name="source" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
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58 <option value="indexed">Use a built-in index</option>
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59 <option value="history">Use one from the history</option>
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60 </param>
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61 <when value="indexed">
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62 <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
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63 <options from_data_table="bowtie_indexes">
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64 <filter type="sort_by" column="2"/>
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65 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
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66 </options>
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67 </param>
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68 </when>
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69 <when value="history">
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70 <param name="own_file" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
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71 </when>
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72 </conditional> <!--param type="data" name="index" label="genome sequence bowtie index"/-->
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73
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74
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75 <param name="gff" type="data" label="gff file" />
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76 <param name="mis" type="integer" value="0" label="number of allowed mismatches when mapping reads to genome" />
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77 <param name="mapnt" type="integer" value="25" label="a read is allowed to map up to this number of positions in the genome" />
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78 <param name="d" type="integer" value="100" label="distance of tag to merged a cluster" />
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79
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80 <param name="p" type="select" lable="cluster method" multiple="false">
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81 <option value="F">conventional</option>
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82 <option value="T">NIBLES</option>
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83 </param>
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84 <param name="l" type="integer" value="1000" label="the length of the upstream and downstream,used in position annotate" />
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86
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87 <conditional name="params">
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88 <param name="function_anno" type="select" label="Do or not annotate siRNAs by function">
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89 <option value="no" selected="true">no</option>
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90 <option value="yes">yes</option>
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91 </param>
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92 <when value="yes">
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93 <param name="nat" type="data" label="atural antisense transcripts file" />
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94 <param name="repeat" type="data" label="repeat information file out of Repeatmasker" />
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95 </when>
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96 </conditional> <!-- params -->
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97
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98 <param name="cen" type="data" label="centromere file input" />
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99 <param name="span" type="integer" value="50000" label="plot span" />
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100
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101 <conditional name="degseq">
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102 <param name="degseq_analysis" type="select" label="Do or not identify Difference Expression Clusters">
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103 <option value="no" selected="true">no</option>
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104 <option value="yes">yes</option>
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105 </param>
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106 <when value="yes">
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107 <param name="deg" type="data" label="file config of de sample" />
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108 </when>
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109 </conditional>
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110
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111 </inputs>
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112
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113 <outputs>
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114 <data format="txt" name="siRNA cluster" from_work_dir="cluster_runs/total.result" label="${tool.name} on ${on_string}: siRNA cluster"/>
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115 <data format="html" name="analysis result" from_work_dir="cluster_runs/result.html" label="${tool.name} on ${on_string}: analysis result"/>
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116
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117 </outputs>
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118
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119 <help>
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120
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121 </help>
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122 </tool>