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annotate piranha.xml @ 0:f7f366ede872 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/piranha commit ba69207568a546d7c3b71a144f78095811e3e99a-dirty
author rnateam
date Fri, 24 Jul 2015 06:05:39 -0400
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0
f7f366ede872 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/piranha commit ba69207568a546d7c3b71a144f78095811e3e99a-dirty
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1 <tool id="piranha" name="Piranha" version="0.1.0">
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2 <description>peak-caller for CLIP- and RIP-Seq data</description>
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3 <requirements>
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4 <requirement type="package" version="1.2.1">piranha</requirement>
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5 </requirements>
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6 <stdio>
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7 <exit_code range="1:" />
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8 </stdio>
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9 <command><![CDATA[
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10 ln -s $input ./foo.$input.ext &&
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11
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12 Piranha
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13 $sort
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14 #if $p_threshold:
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15 -p $p_threshold
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16 #end if
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17 $no_pval_correct
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18 #if $background_thresh:
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19 -a $background_thresh
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20 #end if
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21 #if $bin_size_reponse:
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22 -b $bin_size_reponse
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23 #end if
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24 #if $bin_size_covars:
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25 -i $bin_size_covars
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26 #end if
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27 #if $bin_size_both:
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28 -z $bin_size_both
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29 #end if
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30 #if $merge_bins.merge=="yes":
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31 -u $merge_bins.cluster_dist
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32 #else:
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33 -u $merge_bins.merge
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34 #end if
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35 $print_covars
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36 $fit
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37 #if $dist:
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38 -d $dist
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39 #end if
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40 $fitMethod
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41 #if $model:
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42 -m $model
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43 #end if
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44 $stranded
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45 $no_normalisation
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46 $log_covars
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47 ./foo.$input.ext
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48 #for $covariate in $covariates:
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49 $covariate.covariate_file
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50 #end for
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51
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52 -o ./piranha.out
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53 ]]></command>
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54 <inputs>
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55 <param name="input" type="data" format="bed,bam" label="Choose input BED or BAM file"/>
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56 <repeat name="covariates" title="Choose covariate">
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57 <param name="covariate_file" type="data" format="bed" label="Choose covariate BED file"/>
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58 </repeat>
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59 <param name="sort" type="boolean" label="Is your input file already sorted?" checked="False" falsevalue="-s" truevalue=""/>
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60 <param name="p_threshold" type="float" min="0" max="1" value="1" label="Significance threshold for sites"/>
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61 <param name="no_pval_correct" type="boolean" checked="False" falsevalue="" truevalue="-c"
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62 label="Disable p-values correction for multiple hypothesis testing?" help="We correct by default using B &amp; H."/>
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63 <param name="background_thresh" type="float" optional="true"
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64 label="Indicates that this proportion of the lowest scores should be considered the background"/>
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65 <param name="bin_size_reponse" type="integer" optional="true"
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66 label="Indicates that input is raw reads and should be binned into bins of this size"/>
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67 <param name="bin_size_covars" type="integer" optional="true"
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68 label="Indicates that the covariates are raw reads and should be binned into bins of this size"/>
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69 <param name="bin_size_both" type="integer" optional="true" label="Synonymous with -b x -i x for any x"/>
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70 <conditional name="merge_bins">
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71 <param name="merge" type="select" label="Merge significant bins within certain distance?">
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72 <option value="yes">Yes</option>
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73 <option value="0" selected="true">No</option>
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74 </param>
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75 <when value="yes">
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76 <param name="cluster_dist" type="integer" value="1" label="Merge significant bins within this distance"
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77 help="Default is 1 (merge adjacent)"/>
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78 </when>
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79 </conditional>
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80 <param name="print_covars" type="boolean" checked="True" truevalue="" falsevalue="-r" label="Print covariate values in output" help="(-r)" />
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81 <param name="fit" type="boolean" checked="False" truevalue="-f" falsevalue="" label="Fit only" />
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82 <param name="dist" type="select" label="Select distribution type">
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83 <option value="">None</option>
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84 <option value="Poisson">Poisson</option>
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85 <option value="NegativeBinomial">NegativeBinomial</option>
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86 <option value="ZeroTruncatedPoisson">ZeroTruncatedPoisson</option>
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87 <option value="ZeroTruncatedNegativeBinomial">ZeroTruncatedNegativeBinomial</option>
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88 <option value="PoissonRegression">PoissonRegression</option>
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89 <option value="NegativeBinomialRegression">NegativeBinomialRegression</option>
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90 <option value="ZeroTruncatedPoissonRegression">ZeroTruncatedPoissonRegression</option>
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91 <option value="ZeroTruncatedNegativeBinomialRegression">ZeroTruncatedNegativeBinomialRegression</option>
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92 </param>
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93 <param name="fitMethod" type="boolean" checked="False" truevalue="-t"
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94 falsevalue="" label="Use component fitting method" help="(-t)"/>
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95 <param name="model" type="data" optional="True" format="xml" label="Select the model file"/>
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96
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97 <param name="stranded" type="boolean" checked="True" truevalue=""
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98 falsevalue="-x" label="Preserve strand information"
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99 help="If not set all the peaks will be associated to the positive strand. (-x)"/>
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100 <param name="no_normalisation" type="boolean" checked="yes" falsevalue="-n"
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101 truevalue="" label="Normalise covariates?" help="(-n)"/>
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102 <param name="log_covars" type="boolean" checked="False" truevalue="-l"
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103 falsevalue="" label="Convert covariates to log scale?" help="(-l)"/>
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104 </inputs>
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105 <outputs>
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106 <data format="tabular" name="output_bed" from_work_dir="piranha.out"
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107 label="${tool.name} on ${on_string}: BED with p-values">
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108 <filter>fit is False</filter>
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109 </data>
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110 <data format="xml" name="output_xml" from_work_dir="piranha.out"
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111 label="${tool.name} on ${on_string}: Model file">
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112 <filter>fit is True</filter>
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113 </data>
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114 </outputs>
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115 <tests>
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116 <test>
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117 <param name="input" value="zntbr_unbinned_response.bed" ftype="bed"/>
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118 <repeat name="covariates">
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119 <param name="covariate_file" value="ztnbr_binning_cov1.bed" ftype="bed"/>
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120 </repeat>
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121 <repeat name="covariates">
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122 <param name="covariate_file" value="ztnbr_binning_cov2.bed" ftype="bed"/>
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123 </repeat>
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124 <param name="fit" value="True"/>
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125 <param name="bin_size_reponse" value="1"/>
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126 <param name="background_thresh" value="1"/>
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127 <output name="output_xml" file="ztnbrBinningTestModelOutput.expected.xml" ftype="xml"/>
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128 </test>
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129 <test>
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130 <param name="input" value="testPrianha_zntb_unbinned.bam" ftype="bam"/>
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131 <param name="fit" value="True"/>
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132 <param name="bin_size_reponse" value="1"/>
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133 <param name="background_thresh" value="1"/>
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134 <output name="output_xml" file="ztnbBinningTestModelOutput.expected.xml" ftype="xml"/>
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135 </test>
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136 <test>
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137 <param name="input" value="ztnbSimpleTest_response.bed" ftype="bed"/>
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138 <param name="no_pval_correct" value="True"/>
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139 <param name="p_threshold" value="1"/>
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140 <param name="background_thresh" value="1"/>
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141 <param name="-" value="ZeroTruncatedNegativeBinomial"/>
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142 <output name="output_xml" file="ztnbSimpleTest_output.expected.bed" ftype="tabular"/>
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143 </test>
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144 </tests>
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145 <help><![CDATA[
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146 **What it does**
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147
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148 `Piranha <http://smithlabresearch.org/software/piranha/>`_ is a peak-caller for CLIP- and RIP-Seq data. It takes input in BED or BAM format and identifies regions of statistically significant read enrichment. Additional covariates may optionally be provided to further inform the peak-calling process.
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149
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150
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151 ]]></help>
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152 <citations>
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153 <citation type="bibtex">
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154 @ARTICLE{bgruening_galaxytools,
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155 Author = {Björn Grüning, Cameron Smith, Torsten Houwaart, Nicola Soranzo, Eric Rasche},
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156 keywords = {bioinformatics, ngs, galaxy, cheminformatics, rna},
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157 title = {{Galaxy Tools - A collection of bioinformatics and cheminformatics tools for the Galaxy environment}},
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158 url = {https://github.com/bgruening/galaxytools}
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159 }
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160 </citation>
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161 </citations>
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162 </tool>