Mercurial > repos > iuc > dada2_makesequencetable

comparison dada2_makeSequenceTable.xml @ 2:99c6929236fa draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
author iuc
date Mon, 16 Mar 2020 07:54:26 -0400
parents 9ccec6ed8e82
children 8470de786d47
comparison
equal deleted inserted replaced
1:9ccec6ed8e82 2:99c6929236fa
47 write.data( seqtab, '$stable', "dada2_sequencetable" ) 47 write.data( seqtab, '$stable', "dada2_sequencetable" )
48 ]]></configfile> 48 ]]></configfile>
49 </configfiles> 49 </configfiles>
50 <inputs> 50 <inputs>
51 <param argument="samples" type="data" multiple="true" format="@DADA_UNIQUES@" label="samples" /> 51 <param argument="samples" type="data" multiple="true" format="@DADA_UNIQUES@" label="samples" />
52 <param argument="orderBy" type="select" label="Column order"> 52 <param argument="orderBy" type="select" label="Order ASVs by">
53 <option value="abundance">abundance</option> 53 <option value="abundance">abundance</option>
54 <option value="nsamples">nsamples</option> 54 <option value="nsamples">nsamples</option>
55 </param> 55 </param>
56 <conditional name="filter_cond"> 56 <conditional name="filter_cond">
57 <param name="filter_select" type="select" label="Length filter method"> 57 <param name="filter_select" type="select" label="Length filter method">
72 <filter>plot</filter> 72 <filter>plot</filter>
73 </data> 73 </data>
74 </outputs> 74 </outputs>
75 <tests> 75 <tests>
76 <test expect_num_outputs="2"> 76 <test expect_num_outputs="2">
77 <param name="samples" ftype="dada2_mergepairs" value="mergePairs_F3D0.Rdata"/> 77 <param name="samples" ftype="dada2_mergepairs" value="mergePairs_F3D0_S188_L001.Rdata,mergePairs_F3D141_S207_L001.Rdata"/>
78 <output name="stable" value="makeSequenceTable_F3D0.tab" ftype="dada2_sequencetable" lines_diff="2"/> 78 <output name="stable" value="makeSequenceTable.tab" ftype="dada2_sequencetable" lines_diff="2"/>
79 <output name="plot_output" value="makeSequenceTable_F3D0.pdf" ftype="pdf" compare="sim_size" delta="3000" /> 79 <output name="plot_output" value="makeSequenceTable.pdf" ftype="pdf" compare="sim_size" delta="3000" />
80 </test> 80 </test>
81 <test expect_num_outputs="1"> 81 <test expect_num_outputs="1">
82 <param name="samples" ftype="dada2_mergepairs" value="mergePairs_F3D0.Rdata"/> 82 <param name="samples" ftype="dada2_mergepairs" value="mergePairs_F3D0_S188_L001.Rdata,mergePairs_F3D141_S207_L001.Rdata"/>
83 <param name="filter_cond|filter_select" value="minmax"/> 83 <param name="filter_cond|filter_select" value="minmax"/>
84 <param name="filter_cond|min" value="200"/> 84 <param name="filter_cond|min" value="200"/>
85 <param name="filter_cond|max" value="300"/> 85 <param name="filter_cond|max" value="300"/>
86 <param name="plot" value="no" /> 86 <param name="plot" value="no" />
87 <output name="stable" value="makeSequenceTable_F3D0.tab" ftype="dada2_sequencetable" lines_diff="2" /> 87 <output name="stable" value="makeSequenceTable.tab" ftype="dada2_sequencetable" lines_diff="2" />
88 </test> 88 </test>
89 </tests> 89 </tests>
90 <help><![CDATA[ 90 <help><![CDATA[
91 Description 91 Description
92 ........... 92 ...........