Mercurial > repos > artbio > small_rna_maps

comparison small_rna_maps.xml @ 15:82fedc576024 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c1d96f7f028512aa4d8fcae3dd5f967cd445708e
author artbio
date Sat, 06 Oct 2018 05:24:15 -0400
parents cd75c72e1d75
children 600e2498bd21
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14:cd75c72e1d75 15:82fedc576024
1 <tool id="small_rna_maps" name="small_rna_maps" version="2.5.2"> 1 <tool id="small_rna_maps" name="small_rna_maps" version="2.6.0">
2 <description></description> 2 <description></description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.11.2=py27_0">numpy</requirement> 4 <requirement type="package" version="1.11.2=py27_0">numpy</requirement>
5 <requirement type="package" version="0.11.2.1=py27_0">pysam</requirement> 5 <requirement type="package" version="0.11.2.1=py27_0">pysam</requirement>
6 <requirement type="package" version="1.3.2=r3.3.2_0">r-optparse</requirement> 6 <requirement type="package" version="1.3.2=r3.3.2_0">r-optparse</requirement>
7 <requirement type="package" version="0.6_28=r3.3.2_0">r-latticeextra</requirement> 7 <requirement type="package" version="0.6_28=r3.3.2_0">r-latticeextra</requirement>
8 <requirement type="package" version="2.2.1=r3.3.2_0">r-gridextra</requirement> 8 <requirement type="package" version="2.2.1=r3.3.2_0">r-gridextra</requirement>
9 <requirement type="package" version="1.4.2=r3.3.2_0">r-reshape2</requirement> 9 <requirement type="package" version="1.4.2=r3.3.2_0">r-reshape2</requirement>
10 10 <requirement type="package" version="0.6.6">sambamba</requirement>
11 </requirements> 11 </requirements>
12 <stdio> 12 <stdio>
13 <exit_code range="1:" level="fatal" description="Tool exception" /> 13 <exit_code range="1:" level="fatal" description="Tool exception" />
14 </stdio> 14 </stdio>
15 <command detect_errors="exit_code"><![CDATA[ 15 <command detect_errors="exit_code"><![CDATA[
16 #for $file in $series 16 #for $file in $series
17 samtools index '$file.inputs'; 17 sambamba view -t \${GALAXY_SLOTS} -F "not unmapped and sequence_length >= ${minsize} and sequence_length <= ${maxsize}" -f bam '$file.inputs' >'$file.inputs.name';
18 samtools index '$file.inputs.name';
18 #end for 19 #end for
19 python '$__tool_directory__'/small_rna_maps.py 20 python '$__tool_directory__'/small_rna_maps.py
20 --inputs 21 --inputs
21 #for $file in $series 22 #for $file in $series
22 '$file.inputs' 23 '$file.inputs.name'
23 #end for 24 #end for
24 --sample_names 25 --sample_names
25 #for $sample in $series 26 #for $sample in $series
26 '$sample.inputs.name' 27 '$sample.inputs.name'
27 #end for 28 #end for
37 #else: 38 #else:
38 --plot_methods '${plots_options.first_plot}' 39 --plot_methods '${plots_options.first_plot}'
39 --outputs '$output_tab' ; 40 --outputs '$output_tab' ;
40 #end if 41 #end if
41 Rscript '$__tool_directory__'/small_rna_maps.r 42 Rscript '$__tool_directory__'/small_rna_maps.r
42 --first_dataframe '$output_tab' 43 --first_dataframe '$output_tab'
43 --extra_dataframe '$extra_output_tab' 44 --extra_dataframe '$extra_output_tab'
44 --normalization 45 --normalization
45 #set $norm = "" 46 #set $norm = ""
46 #for $file in $series 47 #for $file in $series
47 #set $norm += str($file.normalization)+' ' 48 #set $norm += str($file.normalization)+' '
48 #end for 49 #end for
49 #set $norm = $norm[:-1] 50 #set $norm = $norm[:-1]
81 value="0" help="If not 0, sets the distance (in nt) below which data are clustered to a single median position" /> 82 value="0" help="If not 0, sets the distance (in nt) below which data are clustered to a single median position" />
82 <conditional name="plots_options"> 83 <conditional name="plots_options">
83 <param name="plots_options_selector" type="select" display="radio" label="Plot Options"> 84 <param name="plots_options_selector" type="select" display="radio" label="Plot Options">
84 <option value="one_plot">Just one plot per chromosome</option> 85 <option value="one_plot">Just one plot per chromosome</option>
85 <option value="two_plot" selected="True">Two plots per chromosome</option> 86 <option value="two_plot" selected="True">Two plots per chromosome</option>
86 <option value="global">Global read size distributions of aligned reads</option> 87 <option value="global">Global read size distributions of aligned reads</option>
87 </param> 88 </param>
88 <when value="two_plot"> 89 <when value="two_plot">
89 <param name="first_plot" type="select" display="radio" label="Select the type of the top plot"> 90 <param name="first_plot" type="select" display="radio" label="Select the type of the top plot">
90 <option value="Counts">Counts</option> 91 <option value="Counts">Counts</option>
91 <option value="Coverage">Coverage</option> 92 <option value="Coverage">Coverage</option>
92 <option value="Mean">Mean Sizes</option> 93 <option value="Mean">Mean Sizes</option>
93 <option value="Median">Median Sizes</option> 94 <option value="Median">Median Sizes</option>
94 <option value="Size">Size Distributions</option> 95 <option value="Size">Size Distributions</option>
95 </param> 96 </param>
96 <param name="extra_plot" type="select" display="radio" label="Select the type of the bottom plot"> 97 <param name="extra_plot" type="select" display="radio" label="Select the type of the bottom plot">
97 <option value="Counts">Counts</option> 98 <option value="Counts">Counts</option>
98 <option value="Coverage">Coverage</option> 99 <option value="Coverage">Coverage</option>
99 <option value="Mean">Mean Sizes</option> 100 <option value="Mean">Mean Sizes</option>
100 <option value="Median">Median Sizes</option> 101 <option value="Median">Median Sizes</option>
101 <option value="Size">Size Distributions</option> 102 <option value="Size">Size Distributions</option>
102 </param> 103 </param>
103 </when> 104 </when>
104 <when value="one_plot"> 105 <when value="one_plot">
105 <param name="first_plot" type="select" display="radio" label="select the type of plot"> 106 <param name="first_plot" type="select" display="radio" label="select the type of plot">
106 <option value="Counts">Counts</option> 107 <option value="Counts">Counts</option>
107 <option value="Coverage">Coverage</option> 108 <option value="Coverage">Coverage</option>
108 <option value="Mean">Mean Sizes</option> 109 <option value="Mean">Mean Sizes</option>
109 <option value="Median">Median Sizes</option> 110 <option value="Median">Median Sizes</option>
110 <option value="Size">Size Distributions</option> 111 <option value="Size">Size Distributions</option>
111 </param> 112 </param>
112 </when> 113 </when>
113 <when value="global"> 114 <when value="global">
132 133
133 <outputs> 134 <outputs>
134 <data format="tabular" name="output_tab" label="$plots_options.first_plot dataframe" /> 135 <data format="tabular" name="output_tab" label="$plots_options.first_plot dataframe" />
135 <data format="tabular" name="extra_output_tab" label="$plots_options.extra_plot dataframe"> 136 <data format="tabular" name="extra_output_tab" label="$plots_options.extra_plot dataframe">
136 <filter>plots_options['plots_options_selector'] == 'two_plot'</filter> 137 <filter>plots_options['plots_options_selector'] == 'two_plot'</filter>
137 </data> 138 </data>
138 <data format="pdf" name="output_pdf" label="small RNA maps" /> 139 <data format="pdf" name="output_pdf" label="small RNA maps" />
139 </outputs> 140 </outputs>
140 141
141 <tests> 142 <tests>
143 <test>
144 <repeat name="series">
145 <param name="inputs" value="input1.bam" ftype="bam" />
146 <param name="normalization" value="1.0" />
147 </repeat>
148 <repeat name="series">
149 <param name="inputs" value="input_new2.bam" ftype="bam" />
150 <param name="normalization" value="2.0" />
151 </repeat>
152 <param name="minsize" value="0" />
153 <param name="maxsize" value="10000" />
154 <param name="cluster" value="0" />
155 <param name="plots_options_selector" value="one_plot" />
156 <param name="first_plot" value="Counts" />
157 <output file="input1_input2new_norm_1_2_counts.tab" name="output_tab" />
158 <output file="input1_input2new_norm_1_2_single_plot_counts.pdf" name="output_pdf" />
159 </test>
142 <test> 160 <test>
143 <repeat name="series"> 161 <repeat name="series">
144 <param name="inputs" value="input1.bam" ftype="bam" /> 162 <param name="inputs" value="input1.bam" ftype="bam" />
145 <param name="normalization" value="1.0" /> 163 <param name="normalization" value="1.0" />
146 </repeat> 164 </repeat>
375 note = {ISBN 978-0-387-75968-5}, 393 note = {ISBN 978-0-387-75968-5},
376 url = {http://lmdvr.r-forge.r-project.org}, 394 url = {http://lmdvr.r-forge.r-project.org},
377 }</citation> 395 }</citation>
378 </citations> 396 </citations>
379 </tool> 397 </tool>
380