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comparison cmbuild.xml @ 8:c9e29ac5d099 draft default tip

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit a812ed8de433ac4e8b42afd636e70cfbb180d2b9"
author bgruening
date Thu, 23 Sep 2021 19:38:58 +0000
parents ee4be6eadd34
children
comparison
equal deleted inserted replaced
7:477d829d3250 8:c9e29ac5d099
1 <tool id="infernal_cmbuild" name="cmbuild" version="@VERSION@.0"> 1 <tool id="infernal_cmbuild" name="cmbuild" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>Build covariance models from sequence alignments</description> 2 <description>Build covariance models from sequence alignments</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <parallelism method="multi" split_inputs="alignment_infile" split_mode="to_size" split_size="10" merge_outputs="cmfile_outfile"></parallelism> 6 <!--parallelism method="multi" split_inputs="alignment_infile" split_mode="to_size" split_size="10" merge_outputs="cmfile_outfile"></parallelism-->
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
8 <expand macro="stdio" /> 8 <expand macro="stdio" />
9 <expand macro="xrefs"/>
9 <command> 10 <command>
10 <![CDATA[ 11 <![CDATA[
11 cmbuild 12 cmbuild
12 -F 13 -F
13 #if $is_summery_output: 14 #if $is_summery_output:
36 --ere $effective_opts.ere 37 --ere $effective_opts.ere
37 #end if 38 #end if
38 #if $effective_opts.eminseq 39 #if $effective_opts.eminseq
39 --eminseq $effective_opts.eminseq 40 --eminseq $effective_opts.eminseq
40 #end if 41 #end if
42 #if $effective_opts.emaxseq
43 --emaxseq $effective_opts.emaxseq
44 #end if
41 #if $effective_opts.ehmmre 45 #if $effective_opts.ehmmre
42 --ehmmre $effective_opts.ehmmre 46 --ehmmre $effective_opts.ehmmre
43 #end if 47 #end if
44 #if $effective_opts.eset 48 #if $effective_opts.eset
45 --eset $effective_opts.eset 49 --eset $effective_opts.eset
148 <param name="ere" type="float" value="" 152 <param name="ere" type="float" value=""
149 label="Set the target mean match state relative entropy" help="(--ere)" optional="true"/> 153 label="Set the target mean match state relative entropy" help="(--ere)" optional="true"/>
150 154
151 <param name="eminseq" type="integer" value="" 155 <param name="eminseq" type="integer" value=""
152 label="Define the minimum allowed effective sequence number" help="(--eminseq)" optional="true"/> 156 label="Define the minimum allowed effective sequence number" help="(--eminseq)" optional="true"/>
157
158 <param name="emaxseq" type="integer" value=""
159 label="Define the maximum allowed effective sequence number" help="(--emaxseq)" optional="true"/>
153 160
154 <param name="ehmmre" type="float" value="" 161 <param name="ehmmre" type="float" value=""
155 label="Set the target HMM mean match state relative entropy" help="(--ehmmre)" optional="true"/> 162 label="Set the target HMM mean match state relative entropy" help="(--ehmmre)" optional="true"/>
156 163
157 <param name="eset" type="integer" value="" 164 <param name="eset" type="integer" value=""
251 </conditional> 258 </conditional>
252 259
253 260
254 </inputs> 261 </inputs>
255 <outputs> 262 <outputs>
256 <data format="text" name="summary_outfile" label="cmbuild summary on ${on_string}"> 263 <data format="txt" name="summary_outfile" label="cmbuild summary on ${on_string}">
257 <filter>is_summery_output is True</filter> 264 <filter>is_summery_output is True</filter>
258 </data> 265 </data>
259 <!--<data format="stockholm" name="annotated_source_alignment_outfile" label="Annotated alignment from ${on_string}"/>--> 266 <!--<data format="stockholm" name="annotated_source_alignment_outfile" label="Annotated alignment from ${on_string}"/>-->
260 <data format="cm" name="cmfile_outfile" label="Covariance models from ${on_string}"/> 267 <data format="cm" name="cmfile_outfile" label="Covariance models from ${on_string}"/>
261 268
322 <param name="alignment_infile" value="cmbuild_input_tRNA5.sto"/> 329 <param name="alignment_infile" value="cmbuild_input_tRNA5.sto"/>
323 <conditional name="Calibrate"> 330 <conditional name="Calibrate">
324 <param name="selector" value="true"/> 331 <param name="selector" value="true"/>
325 <param name="L" value="0.1"/> 332 <param name="L" value="0.1"/>
326 </conditional> 333 </conditional>
327 <output name="outfile"> 334 <output name="cmfile_outfile">
328 <assert_contents> 335 <assert_contents>
329 <has_text text="S 0 -1 0 1 4 0 1 89 109 -7.220 -8.465 -0.063 -4.919"/> 336 <has_text text="S 0 -1 0 1 4 0 1 89 109 -7.220 -8.465 -0.063 -4.919"/>
337 </assert_contents>
338 </output>
339 </test>
340 <!-- Test emax seq parameter -->
341 <test>
342 <param name="alignment_infile" value="cmbuild_input_tRNA5.sto"/>
343 <conditional name="Calibrate">
344 <param name="selector" value="true"/>
345 <param name="L" value="0.1"/>
346 </conditional>
347 <conditional name="effective_opts">
348 <param name="effective_opts_selector" value="--eent"/>
349 <param name="emaxseq" value="100"/>
350 </conditional>
351 <output name="cmfile_outfile">
352 <assert_contents>
353 <has_text text="S 0 -1 0 1 4 0 1 89 109 -7.111 -8.357 -0.068 -4.810"/>
330 </assert_contents> 354 </assert_contents>
331 </output> 355 </output>
332 </test> 356 </test>
333 </tests> 357 </tests>
334 <help> 358 <help>