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comparison deseq2.xml @ 17:d9e5cadc7f0b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit b95582cea8320d5488056a9576474f79cec53be8
author iuc
date Wed, 05 Sep 2018 15:54:03 -0400
parents a416957ee305
children 3bf1b3ec1ddf
comparison
equal deleted inserted replaced
16:a416957ee305 17:d9e5cadc7f0b
62 $header 62 $header
63 63
64 -f '#echo json.dumps(temp_factor_names)#' 64 -f '#echo json.dumps(temp_factor_names)#'
65 -l '#echo json.dumps(filename_to_element_identifiers)#' 65 -l '#echo json.dumps(filename_to_element_identifiers)#'
66 -t $fit_type 66 -t $fit_type
67 #if $batch_factors
68 --batch_factors '$batch_factors'
69 #end if
67 #if $outlier_replace_off: 70 #if $outlier_replace_off:
68 -a 71 -a
69 #end if 72 #end if
70 #if $outlier_filter_off: 73 #if $outlier_filter_off:
71 -b 74 -b
103 </sanitizer> 106 </sanitizer>
104 </param> 107 </param>
105 <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts file(s)"/> 108 <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts file(s)"/>
106 </repeat> 109 </repeat>
107 </repeat> 110 </repeat>
108 111 <param name="batch_factors" type="data" format="tabular" optional="true" label="(Optional) provide a tabular file with additional batch factors to include in the model." help="You can produce this file using RUVSeq or svaseq."/>
109 <param name="header" type="boolean" truevalue="-H" falsevalue="" checked="true" label="Files have header?" help="If this option is set to Yes, the tool will assume that the count files have column headers in the first row. Default: Yes" /> 112 <param name="header" type="boolean" truevalue="-H" falsevalue="" checked="true" label="Files have header?" help="If this option is set to Yes, the tool will assume that the count files have column headers in the first row. Default: Yes" />
110 113
111 <conditional name="tximport"> 114 <conditional name="tximport">
112 <param name="tximport_selector" type="select" label="Choice of Input data"> 115 <param name="tximport_selector" type="select" label="Choice of Input data">
113 <option value="count" selected="True">Count data (e.g. from HTSeq-count, featureCounts or StringTie)</option> 116 <option value="count" selected="True">Count data (e.g. from HTSeq-count, featureCounts or StringTie)</option>
204 <assert_contents> 207 <assert_contents>
205 <has_text_matching expression="FBgn0003360\t1933.9504.*\t-2.8399.*\t0.1309.*-21.6851.*2.831.*8.024" /> 208 <has_text_matching expression="FBgn0003360\t1933.9504.*\t-2.8399.*\t0.1309.*-21.6851.*2.831.*8.024" />
206 </assert_contents> 209 </assert_contents>
207 </output> 210 </output>
208 </test> 211 </test>
212 <!--Ensure additional batch factor correction works -->
213 <test expect_num_outputs="2">
214 <repeat name="rep_factorName">
215 <param name="factorName" value="Treatment"/>
216 <repeat name="rep_factorLevel">
217 <param name="factorLevel" value="Treated"/>
218 <param name="countsFile" value="GSM461179_treat_single.counts,GSM461180_treat_paired.counts,GSM461181_treat_paired.counts"/>
219 </repeat>
220 <repeat name="rep_factorLevel">
221 <param name="factorLevel" value="Untreated"/>
222 <param name="countsFile" value="GSM461176_untreat_single.counts,GSM461177_untreat_paired.counts,GSM461178_untreat_paired.counts,GSM461182_untreat_single.counts"/>
223 </repeat>
224 </repeat>
225 <param name="batch_factors" value="batch_factors.tab"/>
226 <param name="pdf" value="False"/>
227 <param name="normCounts" value="True"/>
228 <output name="deseq_out">
229 <assert_contents>
230 <has_text_matching expression="FBgn0003360\t1933.*\t-2.9.*\t0.1.*\t-26.*\t1.*-152\t4.*-149" />
231 </assert_contents>
232 </output>
233 </test>
209 <!--Ensure counts files without header works --> 234 <!--Ensure counts files without header works -->
210 <test expect_num_outputs="2"> 235 <test expect_num_outputs="2">
211 <repeat name="rep_factorName"> 236 <repeat name="rep_factorName">
212 <param name="factorName" value="Treatment"/> 237 <param name="factorName" value="Treatment"/>
213 <repeat name="rep_factorLevel"> 238 <repeat name="rep_factorLevel">