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comparison samtools_stats.xml @ 6:47035d167365 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 558d30ff047fe2f62658e8b57e27ebe8db77ede1"
author iuc
date Fri, 06 Sep 2019 11:23:05 -0400
parents 5a08c09b9311
children 145f6d74ff5e
comparison
equal deleted inserted replaced
5:5a08c09b9311 6:47035d167365
1 <tool id="samtools_stats" name="Samtools stats" version="2.0.2+galaxy1"> 1 <tool id="samtools_stats" name="Samtools stats" version="2.0.2+galaxy2">
2 <description>generate statistics for BAM dataset</description> 2 <description>generate statistics for BAM dataset</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"> 6 <expand macro="requirements"/>
7 <requirement type="package" version="5.2.3">gnuplot</requirement>
8 <requirement type="package" version="5.26">perl</requirement>
9 </expand>
10 <expand macro="stdio"/> 7 <expand macro="stdio"/>
11 <expand macro="version_command"/> 8 <expand macro="version_command"/>
12 <command><![CDATA[ 9 <command><![CDATA[
13 @ADDTHREADS@ 10 @ADDTHREADS@
14 @PREPARE_IDX@ 11 @PREPARE_IDX@
68 #end if 65 #end if
69 -@ \$addthreads 66 -@ \$addthreads
70 infile 67 infile
71 @REGIONS_MANUAL@ 68 @REGIONS_MANUAL@
72 > '$output' 69 > '$output'
73
74 #if $cond_plot.select_plot=='yes':
75 && plot-bamstats '$output' $cond_plot.log -p '${html_file.files_path}'/
76 && mv '${html_file.files_path}'/index.html '${html_file}'
77 #end if
78 70
79 #if $split_output_cond.split_output_selector == "yes": 71 #if $split_output_cond.split_output_selector == "yes":
80 #set outputs_to_split = str($split_output_cond.generate_tables).split(',') 72 #set outputs_to_split = str($split_output_cond.generate_tables).split(',')
81 && mkdir split 73 && mkdir split
82 #for s in str($split_output_cond.generate_tables).split(','): 74 #for s in str($split_output_cond.generate_tables).split(','):
184 <expand macro="regions_macro"/> 176 <expand macro="regions_macro"/>
185 177
186 <param name="sparse" argument="-x/--sparse" type="boolean" truevalue="-x" falsevalue="" checked="False" label="Suppress absence of insertions" help="Suppress outputting IS rows where there are no insertions."/> 178 <param name="sparse" argument="-x/--sparse" type="boolean" truevalue="-x" falsevalue="" checked="False" label="Suppress absence of insertions" help="Suppress outputting IS rows where there are no insertions."/>
187 <param name="remove_overlaps" argument="-p/--remove-overlaps" type="boolean" truevalue="-p" falsevalue="" checked="False" label="Remove overlaps of paired-end reads from coverage and base count computations" /> 179 <param name="remove_overlaps" argument="-p/--remove-overlaps" type="boolean" truevalue="-p" falsevalue="" checked="False" label="Remove overlaps of paired-end reads from coverage and base count computations" />
188 <param name="cov_threshold" argument="-g/--cov-threshold" optional="true" type="integer" label="Only bases with coverage above this value will be included in the target percentage computation" /> 180 <param name="cov_threshold" argument="-g/--cov-threshold" optional="true" type="integer" label="Only bases with coverage above this value will be included in the target percentage computation" />
189 <conditional name="cond_plot">
190 <param name="select_plot" type="select" label="Generate plots with plot-bamstats">
191 <option value="no" selected="True">No</option>
192 <option value="yes">Yes</option>
193 </param>
194 <when value="no"/>
195 <when value="yes">
196 <param name="log" argument="-l/--log-y" type="boolean" truevalue="-l" falsevalue="" checked="False" label="log scale insert size plot" help="Set the Y axis scale of the Insert Size plot to log 10"/>
197 </when>
198 </conditional>
199 </inputs> 181 </inputs>
200 182
201 <outputs> 183 <outputs>
202 <data name="output" format="tabular" label="${tool.name} on ${on_string}"> 184 <data name="output" format="tabular" label="${tool.name} on ${on_string}">
203 <discover_datasets directory="split" pattern="(?P&lt;designation&gt;.+)\.tab" format="tabular" visible="true" assign_primary_output="true"/> 185 <discover_datasets directory="split" pattern="(?P&lt;designation&gt;.+)\.tab" format="tabular" visible="true" assign_primary_output="true"/>
205 </data> 187 </data>
206 <collection name="output_collection" type="list" label="${tool.name} on ${on_string}"> 188 <collection name="output_collection" type="list" label="${tool.name} on ${on_string}">
207 <discover_datasets directory="split" pattern="(?P&lt;designation&gt;.+)\.tab" format="tabular" visible="false"/> 189 <discover_datasets directory="split" pattern="(?P&lt;designation&gt;.+)\.tab" format="tabular" visible="false"/>
208 <filter>split_output_cond['split_output_selector'] == 'yes'</filter> 190 <filter>split_output_cond['split_output_selector'] == 'yes'</filter>
209 </collection> 191 </collection>
210 <data format="html" name="html_file" label="${tool.name} on ${on_string}: plot-bamstats">
211 <filter>cond_plot['select_plot']=='yes'</filter>
212 </data>
213 </outputs> 192 </outputs>
214 <tests> 193 <tests>
215 <!-- https://github.com/samtools/samtools/blob/9ce8c64493f7ea3fa69bc5c1ac980b1a8e3dcf1f/test/test.pl#L2402 --> 194 <!-- https://github.com/samtools/samtools/blob/9ce8c64493f7ea3fa69bc5c1ac980b1a8e3dcf1f/test/test.pl#L2402 -->
216 <test> 195 <test>
217 <param name="input" value="1_map_cigar.sam" ftype="sam" /> 196 <param name="input" value="1_map_cigar.sam" ftype="sam" />
358 <param name="input" value="samtools_stats_input.bam" ftype="bam" /> 337 <param name="input" value="samtools_stats_input.bam" ftype="bam" />
359 <conditional name="addref_cond"> 338 <conditional name="addref_cond">
360 <param name="addref_select" value="history" /> 339 <param name="addref_select" value="history" />
361 <param name="ref" value="samtools_stats_ref.fa" ftype="fasta" /> 340 <param name="ref" value="samtools_stats_ref.fa" ftype="fasta" />
362 </conditional> 341 </conditional>
363 <conditional name="cond_plot">
364 <param name="select_plot" value="yes"/>
365 </conditional>
366 <output name="output" file="samtools_stats_out1.tab" ftype="tabular" lines_diff="2" /> 342 <output name="output" file="samtools_stats_out1.tab" ftype="tabular" lines_diff="2" />
367 </test> 343 </test>
368 <test> 344 <test>
369 <param name="input" value="samtools_stats_input.bam" ftype="bam" /> 345 <param name="input" value="samtools_stats_input.bam" ftype="bam" />
370 <conditional name="addref_cond"> 346 <conditional name="addref_cond">
384 </tests> 360 </tests>
385 <help><![CDATA[ 361 <help><![CDATA[
386 **What it does** 362 **What it does**
387 363
388 This tool runs the ``samtools stats`` command. 364 This tool runs the ``samtools stats`` command.
365
366 The results of samtools stats can be visualized with MultiQC (for this the default of a single output file needs to be selected).
389 ]]></help> 367 ]]></help>
390 <expand macro="citations"/> 368 <expand macro="citations"/>
391 </tool> 369 </tool>
392 370