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comparison 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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-1:000000000000 0:f7f366ede872
1 <tool id="piranha" name="Piranha" version="0.1.0">
2 <description>peak-caller for CLIP- and RIP-Seq data</description>
3 <requirements>
4 <requirement type="package" version="1.2.1">piranha</requirement>
5 </requirements>
6 <stdio>
7 <exit_code range="1:" />
8 </stdio>
9 <command><![CDATA[
10 ln -s $input ./foo.$input.ext &&
11
12 Piranha
13 $sort
14 #if $p_threshold:
15 -p $p_threshold
16 #end if
17 $no_pval_correct
18 #if $background_thresh:
19 -a $background_thresh
20 #end if
21 #if $bin_size_reponse:
22 -b $bin_size_reponse
23 #end if
24 #if $bin_size_covars:
25 -i $bin_size_covars
26 #end if
27 #if $bin_size_both:
28 -z $bin_size_both
29 #end if
30 #if $merge_bins.merge=="yes":
31 -u $merge_bins.cluster_dist
32 #else:
33 -u $merge_bins.merge
34 #end if
35 $print_covars
36 $fit
37 #if $dist:
38 -d $dist
39 #end if
40 $fitMethod
41 #if $model:
42 -m $model
43 #end if
44 $stranded
45 $no_normalisation
46 $log_covars
47 ./foo.$input.ext
48 #for $covariate in $covariates:
49 $covariate.covariate_file
50 #end for
51
52 -o ./piranha.out
53 ]]></command>
54 <inputs>
55 <param name="input" type="data" format="bed,bam" label="Choose input BED or BAM file"/>
56 <repeat name="covariates" title="Choose covariate">
57 <param name="covariate_file" type="data" format="bed" label="Choose covariate BED file"/>
58 </repeat>
59 <param name="sort" type="boolean" label="Is your input file already sorted?" checked="False" falsevalue="-s" truevalue=""/>
60 <param name="p_threshold" type="float" min="0" max="1" value="1" label="Significance threshold for sites"/>
61 <param name="no_pval_correct" type="boolean" checked="False" falsevalue="" truevalue="-c"
62 label="Disable p-values correction for multiple hypothesis testing?" help="We correct by default using B &amp; H."/>
63 <param name="background_thresh" type="float" optional="true"
64 label="Indicates that this proportion of the lowest scores should be considered the background"/>
65 <param name="bin_size_reponse" type="integer" optional="true"
66 label="Indicates that input is raw reads and should be binned into bins of this size"/>
67 <param name="bin_size_covars" type="integer" optional="true"
68 label="Indicates that the covariates are raw reads and should be binned into bins of this size"/>
69 <param name="bin_size_both" type="integer" optional="true" label="Synonymous with -b x -i x for any x"/>
70 <conditional name="merge_bins">
71 <param name="merge" type="select" label="Merge significant bins within certain distance?">
72 <option value="yes">Yes</option>
73 <option value="0" selected="true">No</option>
74 </param>
75 <when value="yes">
76 <param name="cluster_dist" type="integer" value="1" label="Merge significant bins within this distance"
77 help="Default is 1 (merge adjacent)"/>
78 </when>
79 </conditional>
80 <param name="print_covars" type="boolean" checked="True" truevalue="" falsevalue="-r" label="Print covariate values in output" help="(-r)" />
81 <param name="fit" type="boolean" checked="False" truevalue="-f" falsevalue="" label="Fit only" />
82 <param name="dist" type="select" label="Select distribution type">
83 <option value="">None</option>
84 <option value="Poisson">Poisson</option>
85 <option value="NegativeBinomial">NegativeBinomial</option>
86 <option value="ZeroTruncatedPoisson">ZeroTruncatedPoisson</option>
87 <option value="ZeroTruncatedNegativeBinomial">ZeroTruncatedNegativeBinomial</option>
88 <option value="PoissonRegression">PoissonRegression</option>
89 <option value="NegativeBinomialRegression">NegativeBinomialRegression</option>
90 <option value="ZeroTruncatedPoissonRegression">ZeroTruncatedPoissonRegression</option>
91 <option value="ZeroTruncatedNegativeBinomialRegression">ZeroTruncatedNegativeBinomialRegression</option>
92 </param>
93 <param name="fitMethod" type="boolean" checked="False" truevalue="-t"
94 falsevalue="" label="Use component fitting method" help="(-t)"/>
95 <param name="model" type="data" optional="True" format="xml" label="Select the model file"/>
96
97 <param name="stranded" type="boolean" checked="True" truevalue=""
98 falsevalue="-x" label="Preserve strand information"
99 help="If not set all the peaks will be associated to the positive strand. (-x)"/>
100 <param name="no_normalisation" type="boolean" checked="yes" falsevalue="-n"
101 truevalue="" label="Normalise covariates?" help="(-n)"/>
102 <param name="log_covars" type="boolean" checked="False" truevalue="-l"
103 falsevalue="" label="Convert covariates to log scale?" help="(-l)"/>
104 </inputs>
105 <outputs>
106 <data format="tabular" name="output_bed" from_work_dir="piranha.out"
107 label="${tool.name} on ${on_string}: BED with p-values">
108 <filter>fit is False</filter>
109 </data>
110 <data format="xml" name="output_xml" from_work_dir="piranha.out"
111 label="${tool.name} on ${on_string}: Model file">
112 <filter>fit is True</filter>
113 </data>
114 </outputs>
115 <tests>
116 <test>
117 <param name="input" value="zntbr_unbinned_response.bed" ftype="bed"/>
118 <repeat name="covariates">
119 <param name="covariate_file" value="ztnbr_binning_cov1.bed" ftype="bed"/>
120 </repeat>
121 <repeat name="covariates">
122 <param name="covariate_file" value="ztnbr_binning_cov2.bed" ftype="bed"/>
123 </repeat>
124 <param name="fit" value="True"/>
125 <param name="bin_size_reponse" value="1"/>
126 <param name="background_thresh" value="1"/>
127 <output name="output_xml" file="ztnbrBinningTestModelOutput.expected.xml" ftype="xml"/>
128 </test>
129 <test>
130 <param name="input" value="testPrianha_zntb_unbinned.bam" ftype="bam"/>
131 <param name="fit" value="True"/>
132 <param name="bin_size_reponse" value="1"/>
133 <param name="background_thresh" value="1"/>
134 <output name="output_xml" file="ztnbBinningTestModelOutput.expected.xml" ftype="xml"/>
135 </test>
136 <test>
137 <param name="input" value="ztnbSimpleTest_response.bed" ftype="bed"/>
138 <param name="no_pval_correct" value="True"/>
139 <param name="p_threshold" value="1"/>
140 <param name="background_thresh" value="1"/>
141 <param name="-" value="ZeroTruncatedNegativeBinomial"/>
142 <output name="output_xml" file="ztnbSimpleTest_output.expected.bed" ftype="tabular"/>
143 </test>
144 </tests>
145 <help><![CDATA[
146 **What it does**
147
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.
149
150
151 ]]></help>
152 <citations>
153 <citation type="bibtex">
154 @ARTICLE{bgruening_galaxytools,
155 Author = {Björn Grüning, Cameron Smith, Torsten Houwaart, Nicola Soranzo, Eric Rasche},
156 keywords = {bioinformatics, ngs, galaxy, cheminformatics, rna},
157 title = {{Galaxy Tools - A collection of bioinformatics and cheminformatics tools for the Galaxy environment}},
158 url = {https://github.com/bgruening/galaxytools}
159 }
160 </citation>
161 </citations>
162 </tool>