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comparison multigps.xml @ 50:20687c85887e draft

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Uploaded
author greg
date Mon, 06 Mar 2017 09:17:58 -0500
parents 6997a4b160c5
children 4c5540844bb3
comparison
equal deleted inserted replaced
49:381efb7b880f 50:20687c85887e
1 <tool id="multigps" name="MultiGPS" version="0.73"> 1 <tool id="multigps" name="MultiGPS" version="0.73.0">
2 <description>analyzes collections of multi-condition ChIP-seq data</description> 2 <description>analyzes collections of multi-condition ChIP-seq data</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
147 #end if 147 #end if
148 --edgerod $rbec.edgerod 148 --edgerod $rbec.edgerod
149 --diffp $rbec.diffp 149 --diffp $rbec.diffp
150 #end if 150 #end if
151 #end if 151 #end if
152 >/dev/null
152 --out '$output_html.files_path' 153 --out '$output_html.files_path'
153 && mv $output_dir/*.html $output_html || true 154 && cp $output_dir/*.events.txt '$experiment_events' || true
154 && mv $output_dir/*.table.txt $all_events_table || true 155 && mv $output_dir/*.html '$output_html' || true
155 && mv $output_dir/*.counts $replicates_counts || true 156 && mv $output_dir/*.table.txt '$all_events_table' || true
157 && mv $output_dir/*.counts '$replicates_counts' || true
156 ]]> 158 ]]>
157 </command> 159 </command>
158 <inputs> 160 <inputs>
159 <param name="expt" type="data" format="bam,bed,scidx" label="Run MultiGPS on"> 161 <param name="expt" type="data" format="bam,bed,scidx" label="Run MultiGPS on">
160 <validator type="unspecified_build" /> 162 <validator type="unspecified_build" />
354 </when> 356 </when>
355 <when value="hide" /> 357 <when value="hide" />
356 </conditional> 358 </conditional>
357 </inputs> 359 </inputs>
358 <outputs> 360 <outputs>
359 <data name="output_html" format="html" label="Results (HTML) on ${on_string}"/> 361 <data name="replicates_counts" format="tabular" label="${tool.name} replicates counts on ${on_string}"/>
360 <data name="all_events_table" format="tabular" label="All events table on ${on_string}"/> 362 <data name="all_events_table" format="tabular" label="${tool.name} all events table on ${on_string}"/>
361 <data name="replicates_counts" format="tabular" label="Replicates counts on ${on_string}"/> 363 <data name="experiment_events" format="tabular" label="${tool.name} experiment events on ${on_string}"/>
364 <data name="output_html" format="html" label="${tool.name} on ${on_string}"/>
362 </outputs> 365 </outputs>
363 <tests> 366 <tests>
364 <test> 367 <test>
365 <param name="expt" value="expt_hg19.scidx" ftype="scidx" dbkey="hg19" /> 368 <param name="expt" value="expt_hg19.scidx" ftype="scidx" dbkey="hg19" />
366 <param name="advanced_options_cond" value="hide" /> 369 <param name="advanced_options_cond" value="hide" />