Mercurial > repos > iuc > dada2_seqcounts

comparison dada2_seqCounts.xml @ 2:d006780246bf 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 11:30:35 +0000
parents 448c54392221
children 41006d6914cd
comparison
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1:718ca97bdd8c 2:d006780246bf
87 <!-- test for the separate inputs (didn't implement as single test using the repeat 87 <!-- test for the separate inputs (didn't implement as single test using the repeat
88 since the sample name won't match anyway [galaxy does not allow to specify the 88 since the sample name won't match anyway [galaxy does not allow to specify the
89 names of the elements of the input collection for <param ... multiple="true">]) --> 89 names of the elements of the input collection for <param ... multiple="true">]) -->
90 <test> 90 <test>
91 <repeat name="inrep"> 91 <repeat name="inrep">
92 <param name="input" value="filterAndTrim_F3D0.tab" ftype="tabular"/> 92 <param name="input" value="F3D0_S188_L001_R1_001.tab" ftype="tabular"/>
93 <param name="name" value="filter"/> 93 <param name="name" value="filter"/>
94 </repeat> 94 </repeat>
95 <output name="counts" value="seqCounts_F3D0_filter.tab" ftype="tabular" /> 95 <output name="counts" value="seqCounts_filter.tab" ftype="tabular" />
96 </test> 96 </test>
97 <test> 97 <test>
98 <repeat name="inrep"> 98 <repeat name="inrep">
99 <param name="input" value="dada_F3D0_R1.Rdata" ftype="dada2_dada"/> 99 <param name="input" value="dada_F3D0_S188_L001_R1.Rdata,dada_F3D141_S207_L001_R1.Rdata" ftype="dada2_dada"/>
100 <param name="name" value="dadaF"/> 100 <param name="name" value="dadaF"/>
101 </repeat> 101 </repeat>
102 <output name="counts" value="seqCounts_F3D0_dadaF.tab" ftype="tabular" /> 102 <output name="counts" value="seqCounts_dadaF.tab" ftype="tabular" />
103 </test> 103 </test>
104 <test> 104 <test>
105 <repeat name="inrep"> 105 <repeat name="inrep">
106 <param name="input" value="mergePairs_F3D0.Rdata" ftype="dada2_mergepairs"/> 106 <param name="input" value="mergePairs_F3D0_S188_L001.Rdata,mergePairs_F3D141_S207_L001.Rdata" ftype="dada2_mergepairs"/>
107 <param name="name" value="merge"/> 107 <param name="name" value="merge"/>
108 </repeat> 108 </repeat>
109 <output name="counts" value="seqCounts_F3D0_merge.tab" ftype="tabular" /> 109 <output name="counts" value="seqCounts_merge.tab" ftype="tabular" />
110 </test> 110 </test>
111 <test> 111 <test>
112 <repeat name="inrep"> 112 <repeat name="inrep">
113 <param name="input" value="makeSequenceTable_F3D0.tab" ftype="dada2_sequencetable"/> 113 <param name="input" value="makeSequenceTable.tab" ftype="dada2_sequencetable"/>
114 <param name="name" value="seqtab"/> 114 <param name="name" value="seqtab"/>
115 </repeat> 115 </repeat>
116 <output name="counts" value="seqCounts_F3D0_seqtab.tab" ftype="tabular" /> 116 <output name="counts" value="seqCounts_seqtab.tab" ftype="tabular" />
117 </test> 117 </test>
118 <test> 118 <test>
119 <repeat name="inrep"> 119 <repeat name="inrep">
120 <param name="input" value="removeBimeraDenovo_F3D0.tab" ftype="dada2_sequencetable"/> 120 <param name="input" value="removeBimeraDenovo.tab" ftype="dada2_sequencetable"/>
121 <param name="name" value="nochim"/> 121 <param name="name" value="nochim"/>
122 </repeat> 122 </repeat>
123 <output name="counts" value="seqCounts_F3D0_nochim.tab" ftype="tabular" /> 123 <output name="counts" value="seqCounts_nochim.tab" ftype="tabular" />
124 </test> 124 </test>
125 </tests> 125 </tests>
126 <help><![CDATA[ 126 <help><![CDATA[
127 Description 127 Description
128 ........... 128 ...........
133 ..... 133 .....
134 134
135 **Inputs:** 135 **Inputs:**
136 136
137 Any number of results of dada2 steps in the following form: 137 Any number of results of dada2 steps in the following form:
138 - a collection of results from dada, or mergePairs; or the collection of statistics from filterAndTrim (the identifiers of the collection elements are used as sample names) 138
139
140 - a collection of results from dada, mergePairs, or the collection of statistics from filterAndTrim (the identifiers of the collection elements are used as sample names)
141 - the results of dada in non-batch mode
139 - the result of makeSequenceTable or removeBimeraDenovo 142 - the result of makeSequenceTable or removeBimeraDenovo
140 143
141 **Output:** 144 **Output:**
142 145
143 A table containing the number of sequences per sample (rows) for each input (columns) 146 A table containing the number of sequences per sample (rows) for each input (columns)