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comparison jbrowse.xml @ 19:8f33c9fbc119 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
author iuc
date Fri, 06 Jul 2018 06:10:18 -0400
parents 836d1aa3e89a
children 1c718d8b3532
comparison
equal deleted inserted replaced
18:836d1aa3e89a 19:8f33c9fbc119
1 <tool id="jbrowse" name="JBrowse" version="@WRAPPER_VERSION@.3"> 1 <tool id="jbrowse" name="JBrowse" version="@TOOL_VERSION@+@WRAPPER_VERSION@">
2 <description>genome browser</description> 2 <description>genome browser</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"/>
599 <param name="reference_genome|genome_type_select" value="history"/> 599 <param name="reference_genome|genome_type_select" value="history"/>
600 <param name="reference_genome|genomes" value="merlin.fa"/> 600 <param name="reference_genome|genomes" value="merlin.fa"/>
601 <param name="gencode" value="1" /> 601 <param name="gencode" value="1" />
602 <param name="standalone" value="Data Directory" /> 602 <param name="standalone" value="Data Directory" />
603 <param name="uglyTestingHack" value="enabled" /> 603 <param name="uglyTestingHack" value="enabled" />
604 <output name="output" file="gencode/test-1.xml" lines_diff="4" /> 604 <output name="output" file="gencode/test-1.xml" lines_diff="14"/>
605 </test> 605 </test>
606 <test> 606 <test>
607 <param name="reference_genome|genome_type_select" value="history"/> 607 <param name="reference_genome|genome_type_select" value="history"/>
608 <param name="reference_genome|genomes" value="merlin.fa"/> 608 <param name="reference_genome|genomes" value="merlin.fa"/>
609 <param name="gencode" value="11" /> 609 <param name="gencode" value="11" />
803 </conditional> 803 </conditional>
804 </repeat> 804 </repeat>
805 </repeat> 805 </repeat>
806 806
807 <param name="uglyTestingHack" value="enabled" /> 807 <param name="uglyTestingHack" value="enabled" />
808 <output name="output" file="gff3/test.xml" lines_diff="64" /> 808 <output name="output" file="gff3/test.xml" lines_diff="256" />
809 </test> 809 </test>
810 <test> 810 <test>
811 <param name="reference_genome|genome_type_select" value="history"/> 811 <param name="reference_genome|genome_type_select" value="history"/>
812 <param name="reference_genome|genomes" value="merlin.fa"/> 812 <param name="reference_genome|genomes" value="merlin.fa"/>
813 <param name="gencode" value="11" /> 813 <param name="gencode" value="11" />
906 906
907 <param name="uglyTestingHack" value="enabled" /> 907 <param name="uglyTestingHack" value="enabled" />
908 <output name="output" file="track_config/test.xml" lines_diff="26"/> 908 <output name="output" file="track_config/test.xml" lines_diff="26"/>
909 </test> 909 </test>
910 <test> 910 <test>
911 <param name="reference_genome|genome_type_select" value="history"/>
912 <param name="reference_genome|genomes" value="merlin.fa"/>
913 <param name="gencode" value="11" />
914 <param name="standalone" value="Data Directory" />
915
916 <repeat name="track_groups">
917 <param name="category" value="Auto Coloured" />
918 <repeat name="data_tracks">
919 <conditional name="data_format">
920 <param name="data_format_select" value="pileup"/>
921 <param name="annotation" value="bam/merlin-sample.bam"/>
922 </conditional>
923 </repeat>
924 </repeat>
925
926 <param name="uglyTestingHack" value="enabled" />
927 <output name="output" file="bam/test.xml" lines_diff="48"/>
928 </test>
929
930 <test>
911 <!-- data_table --> 931 <!-- data_table -->
912 <param name="reference_genome|genome_type_select" value="indexed"/> 932 <param name="reference_genome|genome_type_select" value="indexed"/>
913 <param name="reference_genome|genomes" value="merlin"/> 933 <param name="reference_genome|genomes" value="merlin"/>
914 <param name="gencode" value="1" /> 934 <param name="gencode" value="1" />
915 <param name="standalone" value="Data Directory" /> 935 <param name="standalone" value="Data Directory" />
916 <param name="uglyTestingHack" value="enabled" /> 936 <param name="uglyTestingHack" value="enabled" />
917 <output name="output" file="gencode/test-data_table.xml" lines_diff="4" /> 937 <output name="output" file="gencode/test-data_table.xml" lines_diff="6" />
918 </test> 938 </test>
919 </tests> 939 </tests>
920 <help><![CDATA[ 940 <help><![CDATA[
921 JBrowse-in-Galaxy 941 JBrowse-in-Galaxy
922 ================= 942 =================