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comparison peakachu.xml @ 1:09c51ff142a2 draft

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planemo upload for repository https://github.com/tbischler/PEAKachu commit 172dab2fc73fcce3ae7df19286b48848af9033d2-dirty
author rnateam
date Tue, 22 May 2018 11:43:54 -0400
parents ba2996b5f69c
children 26304ccaca57
comparison
equal deleted inserted replaced
0:ba2996b5f69c 1:09c51ff142a2
1 <tool id="peakachu" name="PEAKachu" version="0.1.0.0"> 1 <tool id="peakachu" name="PEAKachu" version="0.1.0.1">
2 <description>Calls Peaks in CLIP data</description> 2 <description>Calls Peaks in CLIP data</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="3.6">python</requirement> 4 <requirement type="package" version="3.6">python</requirement>
5 <requirement type="package" version="0.1.0">peakachu</requirement> 5 <requirement type="package" version="0.1.0">peakachu</requirement>
6 </requirements> 6 </requirements>
63 --mad_multiplier $mad_multiplier 63 --mad_multiplier $mad_multiplier
64 --fc_cutoff $fc_cutoff 64 --fc_cutoff $fc_cutoff
65 --padj_threshold $padj_threshold 65 --padj_threshold $padj_threshold
66 66
67 && 67 &&
68 head -n 1 -q ./tmp_output/peak_tables/*.csv | head -n 1 > peaks.tsv && 68 if ls ./tmp_output/peak_tables/*.csv > /dev/null;
69 tail -n +2 -q ./tmp_output/peak_tables/*.csv >> peaks.tsv && 69 then
70 mv peaks.tsv '$peak_tables' && 70 head -n 1 -q ./tmp_output/peak_tables/*.csv | head -n 1 > peaks.tsv &&
71 mv ./tmp_output/plots/Initial*.png '$MA_plot' 71 tail -n +2 -q ./tmp_output/peak_tables/*.csv >> peaks.tsv &&
72 mv peaks.tsv '$peak_tables' &&
73 cat ./tmp_output/peak_annotations/*.gff | awk '/peak/ {print $0}' > peak_annotations.gff &&
74 mv peak_annotations.gff '$peak_annotations' &&
75 mv ./tmp_output/plots/Initial*.png '$MA_plot';
76 else
77 echo "No Peaks Found" >&2;
78 fi
79
72 80
73 ]]> 81 ]]>
74 </command> 82 </command>
75 <inputs> 83 <inputs>
76 <param name="experimentLibs" type="data" format="bam" label="Experiment Libraries" multiple="True"/> 84 <param name="experimentLibs" type="data" format="bam" label="Experiment Libraries" multiple="True"/>
155 <param argument="--fc_cutoff" label="Fold Change Threshold" type="float" value="2.0"/> 163 <param argument="--fc_cutoff" label="Fold Change Threshold" type="float" value="2.0"/>
156 <param argument="--padj_threshold" type="float" label="Adjusted p-value Threshold" value="0.05"/> 164 <param argument="--padj_threshold" type="float" label="Adjusted p-value Threshold" value="0.05"/>
157 </inputs> 165 </inputs>
158 <outputs> 166 <outputs>
159 <data format="tabular" name="peak_tables" label="${tool.name} ${mode.mode_selector} on ${on_string}: peaks"/> 167 <data format="tabular" name="peak_tables" label="${tool.name} ${mode.mode_selector} on ${on_string}: peaks"/>
168 <data format="gff" name="peak_annotations" label="${tool.name} ${mode.mode_selector} on ${on_string}: peak_annotations"/>
160 <data format="png" name="MA_plot" label="${tool.name} ${mode.mode_selector} on ${on_string}: MA plot"/> 169 <data format="png" name="MA_plot" label="${tool.name} ${mode.mode_selector} on ${on_string}: MA plot"/>
161 </outputs> 170 </outputs>
162 <tests> 171 <tests>
163 <test> 172 <test>
164 <param name="experimentLibs" value="test1_+xl.bam"/> 173 <param name="experimentLibs" value="test1_+xl.bam"/>
165 <param name="controlLibs" value="test1_-xl.bam"/> 174 <param name="controlLibs" value="test1_-xl.bam"/>
166 <output name="peak_tables" ftype="tabular" file="test1_peaks.tsv"/> 175 <output name="peak_tables" ftype="tabular" file="test1_peaks.tsv"/>
167 <output name="MA_plot" ftype="png" file="test1_MA.png"/> 176 <output name="peak_annotations" ftype="gff" file="test1_peak_annotations.gff"/>
168 </test> 177 </test>
169 </tests> 178 </tests>
170 <help> 179 <help>
171 <![CDATA[ 180 <![CDATA[
172 **PEAKachu** 181 **PEAKachu**