Mercurial > repos > simon-gladman > phyloseq_filter

comparison phyloseq_filter.xml @ 2:54897b7e0551 draft default tip

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Updated tool
author simon-gladman
date Thu, 22 Nov 2018 08:13:52 -0500
parents 9fbb104e16d9
children
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1:9fbb104e16d9 2:54897b7e0551
52 <option value="Family">Family</option> 52 <option value="Family">Family</option>
53 <option value="Genus">Genus</option> 53 <option value="Genus">Genus</option>
54 <option value="Species">Species</option> 54 <option value="Species">Species</option>
55 </param> 55 </param>
56 <param name="keep" size="10" type="integer" value="5" label="Number of the most abundant taxonomic rank units to keep in the filtered BIOM file" help="e.g. Phyla, Class and etc. as specified above. Select a value > 1."/> 56 <param name="keep" size="10" type="integer" value="5" label="Number of the most abundant taxonomic rank units to keep in the filtered BIOM file" help="e.g. Phyla, Class and etc. as specified above. Select a value > 1."/>
57 <param name="cutoff" size="10" type="integer" value="5" label="Filter out OTUs. Remove OTUs from the analysis that do not appear more than X times in more than Y% of the samples. Specify value of X" help="Remove OTUs that do not appear more than X times (e.g., 5 times)"/> 57 <param name="cutoff" size="10" type="integer" value="1" label="Filter out OTUs. Remove OTUs from the analysis that do not appear more than X times in more than Y% of the samples. Specify value of X" help="Remove OTUs that do not appear more than X times (e.g., 5 times)"/>
58 <param name="nsample" size="10" type="float" value="0.5" label="Specify value of Y (where 1.0 = 100%)"/> 58 <param name="nsample" size="10" type="float" value="0.0" label="Specify value of Y (where 1.0 = 100%)"/>
59 </inputs> 59 </inputs>
60 60
61 <outputs> 61 <outputs>
62 <data format="biom1" name="outputbiom" label="${tool.name} on ${on_string}.biom"/> 62 <data format="biom1" name="outputbiom" label="${tool.name} on ${on_string}.biom"/>
63 <data format="html" name="htmlfile" label="${tool.name} on ${on_string} Sample Abundance plot.html"/> 63 <data format="html" name="htmlfile" label="${tool.name} on ${on_string} Sample Abundance plot.html"/>
68 <conditional name="file_source"> 68 <conditional name="file_source">
69 <param name="file_source_selector" value="set_biom"/> 69 <param name="file_source_selector" value="set_biom"/>
70 <param name="input" value="GP.biom" ftype="biom1"/> 70 <param name="input" value="GP.biom" ftype="biom1"/>
71 </conditional> 71 </conditional>
72 <output name="htmlfile" ftype="html" file="biom_out.html" /> 72 <output name="htmlfile" ftype="html" file="biom_out.html" />
73 <output name="outputbiom" file="out.biom" lines_diff="2" ftype="biom1"/> 73 <output name="outputbiom" >
74 <!-- <assert_contents> 74 <assert_contents>
75 <has_text text="Biological Observation Matrix"/> 75 <has_text text="Biological Observation Matrix"/>
76 </assert_contents> 76 </assert_contents>
77 </output> --> 77 </output>
78 </test> 78 </test>
79 <test> <!-- Test #2: Test TABULAR format inputs --> 79 <test> <!-- Test #2: Test TABULAR format inputs -->
80 <conditional name="file_source"> 80 <conditional name="file_source">
81 <param name="file_source_selector" value="set_table" /> 81 <param name="file_source_selector" value="set_table" />
82 <param name="OTU_TABLE" value="GP_OTU_TABLE.txt" /> 82 <param name="OTU_TABLE" value="GP_OTU_TABLE.txt" />