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annotate diffbind.xml @ 3:d6dcb3dd5f8f draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diffbind commit 78d26b3a3bbaf30d4d1367a0361618876fe69ae7
author bgruening
date Tue, 08 Mar 2016 08:13:00 -0500
parents 492d5ac7b2e2
children 69138bfd8644
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1 <tool id="diffbind" name="DiffBind" version="2.1.0">
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2 <description> differential binding analysis of ChIP-Seq peak data</description>
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3 <requirements>
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4 <requirement type="binary">Rscript</requirement>
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5 <requirement type="R-module">DESeq2</requirement>
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6 <requirement type="package" version="3.0.3">R</requirement>
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7 <requirement type="package" version="1.2.10">deseq2</requirement>
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8 <requirement type="package" version="1.8.3">diffbind</requirement>
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9 </requirements>
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10 <stdio>
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11 <regex match="Execution halted"
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12 source="both"
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13 level="fatal"
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14 description="Execution halted." />
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15 <regex match="Input-Error 01"
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16 source="both"
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17 level="fatal"
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18 description="Error in your input parameters: Make sure you only apply factors to selected samples." />
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19 <regex match="Error in"
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20 source="both"
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21 level="fatal"
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22 description="An undefined error occured, please check your intput carefully and contact your administrator." />
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23 </stdio>
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24 <command>
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25 <![CDATA[
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26 ## seems that diffbind also needs file extensions to work properly
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27 #set $counter = 1
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28 #for $sample in $samples:
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29 ln -s $sample.bamreads #echo str($counter) + "_bamreads.bam"# &&
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30 ln -s ${sample.bamreads.metadata.bam_index} #echo str($counter) + "_bamreads.bai"# &&
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31 #if str( $sample.bamcontrol ) != 'None':
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32 ln -s $sample.bamcontrol #echo str($counter) + "_bamcontrol.bam"# &&
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33 ln -s ${sample.bamcontrol.metadata.bam_index} #echo str($counter) + "_bamcontrol.bai"# &&
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34 #end if
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35 #set $counter = $counter + 1
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36 #end for
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37
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38 Rscript $__tool_directory__/diffbind.R
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39 -i $infile
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40 -o $outfile
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41 -p $plots
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42 -f $format
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43 ]]>
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44 </command>
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45 <configfiles>
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46 <configfile name="infile">
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47 #set $counter = 1
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48 #for $sample in $samples:
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49 #if str( $sample.bamcontrol ) != 'None' and $counter == 1:
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50 SampleID,Tissue,Factor,Condition,Replicate,bamReads,bamControl,Peaks
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51 #elif $counter == 1:
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52 SampleID,Tissue,Factor,Condition,Replicate,bamReads,Peaks
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53 #end if
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54 #if str( $sample.bamcontrol ) != 'None':
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55 $sample.sample_id,$sample.tissue,$sample.factor,$sample.condition,$sample.replicate,#echo str($counter) + '_bamreads.bam'#,#echo str($counter) + '_bamcontrol.bam'#,$sample.peaks
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56 #else:
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57 $sample.sample_id,$sample.tissue,$sample.factor,$sample.condition,$sample.replicate,#echo str($counter) + '_bamreads.bam'#,$sample.peaks
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58 #end if
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59 #set $counter = $counter + 1
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60 #end for
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61 </configfile>
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62 </configfiles>
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63 <inputs>
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64 <repeat name="samples" title="Samples" min="2">
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65 <param name="sample_id" type="text" value="Sample ID" label="Specify a sample id" help="e.g. BT474.1-" />
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66 <param name="tissue" type="text" value="Tissue" label="Specify the tissue" help="e.g. BT474" />
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67 <param name="factor" type="text" value="Factor Name" label="Specify a factor name" help="e.g. ER" />
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68 <param name="condition" type="text" value="Condition" label="Specify the condition" help="e.g. Resistent" />
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69 <param name="replicate" type="integer" value="1" label="Specify the replicate number" help="e.g. 1" />
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70 <param format="bam" name="bamreads" type="data" label="Read BAM file" help="Specify the Read BAM file, used for Peak calling."/>
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71 <param format="bam" name="bamcontrol" type="data" optional="True" label="Control BAM file" help="If specifying a control BAM file for this sample, then all samples are required to specify one."/>
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72 <param format="bed" name="peaks" type="data" label="Peak file" help="Result of your Peak calling experiment."/>
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73 </repeat>
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74 <param name="pdf" type="boolean" truevalue="" falsevalue="" checked="true"
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75 label="Visualising the analysis results"
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76 help="output an additional PDF files" />
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77 <param name="format" type="select" label="Output Format">
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78 <option value="bed">BED</option>
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79 <option value="gff">GFF</option>
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80 <option value="wig">WIG</option>
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81 </param>
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82 </inputs>
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83 <outputs>
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84 <data format="bed" name="outfile" label="Differential binding sites on ${on_string}">
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85 <change_format>
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86 <when input="format" value="wig" format="wig" />
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87 <when input="format" value="gff" format="gff" />
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88 </change_format>
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89 </data>
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90 <data format="pdf" name="plots" label="Differential binding sites on ${on_string}">
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91 <filter>pdf == True</filter>
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92 </data>
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93 </outputs>
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94 <help>
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95 <![CDATA[
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96
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97 What it does
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98 ************
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99
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100 Diffbind provides functions for processing ChIP-Seq data enriched for genomic loci where specific protein/DNA binding occurs, including peak sets identified by ChIP-Seq peak callers and aligned sequence read datasets.
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101
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102 Input
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103 *****
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104
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105 * You have to specify your samples. Here is one example::
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106
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107 ID Tissue Factor Condition Treatment Replicate Caller Intervals
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108 BT4741 BT474 ER Resistant Full-Media 1 raw 1084
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109
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110 * BAM file which contains the mapped sequencing reads can be associated with each peakset
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111 * Control BAM file represents a control dataset and are optional, but have to specified for all when used.
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112 * Peak file: Result of your Peak calling experiment
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113
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114 Output
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115 ******
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116
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117 As output format you can choose BED, GFF, WIG.
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118
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119 References
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120 **********
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121
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122 DiffBind_ Authors: Rory Stark, Gordon Brown (2011)
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123
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124 .. _DiffBind: http://www.bioconductor.org/packages/release/bioc/html/DiffBind.html
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125
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126 Wrapper authors: Bjoern Gruening, Pavankumar Videm
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127
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128 ]]>
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129 </help>
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130 <citations>
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131 <citation type="doi">doi:10.1038/nature10730</citation>
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132 </citations>
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133 </tool>