Mercurial > repos > iuc > mothur_chimera_vsearch

comparison chimera.vsearch.xml @ 7:de3cfb122105 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit dfdd4c590370ecb3a9806314d43eb5668e36a01a"
author iuc
date Fri, 22 Jan 2021 01:09:52 +0000
parents b4e60c1d77ac
children bdb4a58a2025
comparison
equal deleted inserted replaced
6:12e856482d26 7:de3cfb122105
1 <tool profile="16.07" id="mothur_chimera_vsearch" name="Chimera.vsearch" version="@WRAPPER_VERSION@.1"> 1 <tool profile="16.07" id="mothur_chimera_vsearch" name="Chimera.vsearch" version="@WRAPPER_VERSION@.2">
2 <description>find potential chimeric sequences using vsearch</description> 2 <description>find potential chimeric sequences using vsearch</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">
99 <outputs> 99 <outputs>
100 <expand macro="logfile-output"/> 100 <expand macro="logfile-output"/>
101 <data name="vsearch.chimeras" format="txt" from_work_dir="fasta.*vsearch.chimeras" label="${tool.name} on ${on_string}: vsearch.chimeras"/> 101 <data name="vsearch.chimeras" format="txt" from_work_dir="fasta.*vsearch.chimeras" label="${tool.name} on ${on_string}: vsearch.chimeras"/>
102 <data name="out_accnos" format="mothur.accnos" from_work_dir="fasta.*vsearch.accnos" label="${tool.name} on ${on_string}: vsearch.accnos"/> 102 <data name="out_accnos" format="mothur.accnos" from_work_dir="fasta.*vsearch.accnos" label="${tool.name} on ${on_string}: vsearch.accnos"/>
103 <data name="out_count" format="mothur.count_table" from_work_dir="template.*vsearch.pick.count_table" label="${tool.name} on ${on_string}: vsearch.count_table"> 103 <data name="out_count" format="mothur.count_table" from_work_dir="template.*vsearch.pick.count_table" label="${tool.name} on ${on_string}: vsearch.count_table">
104 <filter>template['source'] == 'self' and template['count']</filter> 104 <filter>template['source'] == 'self' and template['count'] and template['count'].metadata.groups != []</filter>
105 </data> 105 </data>
106 </outputs> 106 </outputs>
107 <tests> 107 <tests>
108 <test><!-- de novo test with name file --> 108 <test expect_num_outputs="3"><!-- de novo test with name file -->
109 <param name="fasta" value="stool_small.unique.fasta"/> 109 <param name="fasta" value="stool_small.unique.fasta"/>
110 <param name="source" value="names"/> 110 <param name="source" value="names"/>
111 <param name="name" value="stool_small.names"/> 111 <param name="name" value="stool_small.names"/>
112 <output name="vsearch.chimeras" file="stool_small.vsearch.chimeras" ftype="txt"/> 112 <output name="vsearch.chimeras" file="stool_small.vsearch.chimeras" ftype="txt"/>
113 <output name="out_accnos" file="stool_small.denovo.vsearch.accnos" ftype="mothur.accnos"/> 113 <output name="out_accnos" file="stool_small.denovo.vsearch.accnos" ftype="mothur.accnos"/>
114 <param name="savelog" value="true"/> 114 <param name="savelog" value="true"/>
115 <expand macro="logfile-test"/> 115 <expand macro="logfile-test"/>
116 </test> 116 </test>
117 <test><!-- de novo test with count table--> 117 <test expect_num_outputs="4"><!-- de novo test with count table-->
118 <param name="fasta" value="chimera.fasta"/> 118 <param name="fasta" value="chimera.fasta"/>
119 <param name="source" value="self"/> 119 <param name="source" value="self"/>
120 <param name="count" value="chimera.count_table"/> 120 <param name="count" value="chimera.count_table" ftype="mothur.count_table"/>
121 <param name="dereplicate" value="true"/> 121 <param name="dereplicate" value="true"/>
122 <output name="vsearch.chimeras" file="chimera.vsearch.chimeras" ftype="txt"/> 122 <output name="vsearch.chimeras" file="chimera.vsearch.chimeras" ftype="txt"/>
123 <output name="out_accnos" file="chimera.vsearch.accnos" ftype="mothur.accnos"/> 123 <output name="out_accnos" file="chimera.vsearch.accnos" ftype="mothur.accnos" sort="true"/>
124 <output name="out_count" file="chimera.vsearch.count_table" ftype="mothur.count_table"/> 124 <output name="out_count" file="chimera.vsearch.count_table" ftype="mothur.count_table"/>
125 <param name="savelog" value="true"/> 125 <param name="savelog" value="true"/>
126 <expand macro="logfile-test"/> 126 <expand macro="logfile-test"/>
127 </test> 127 </test>
128 <test><!-- test with reference file --> 128 <test expect_num_outputs="3"><!-- de novo test with count table (missing group info)-->
129 <param name="fasta" value="chimera.fasta"/>
130 <param name="source" value="self"/>
131 <param name="count" value="chimera.count_table_wogroups" ftype="mothur.count_table"/>
132 <param name="dereplicate" value="true"/>
133 <!-- for some reason only for count tables wo group info header is printed -->
134 <output name="vsearch.chimeras" file="chimera.vsearch.chimeras_wogroups" ftype="txt"/>
135 <output name="out_accnos" file="chimera.vsearch.accnos" ftype="mothur.accnos" sort="true"/>
136 <param name="savelog" value="true"/>
137 <expand macro="logfile-test"/>
138 </test>
139 <test expect_num_outputs="3"><!-- test with reference file -->
129 <param name="fasta" value="stool_small.unique.fasta"/> 140 <param name="fasta" value="stool_small.unique.fasta"/>
130 <param name="source" value="hist"/> 141 <param name="source" value="hist"/>
131 <param name="reference" value="stool_small.unique.fasta"/> 142 <param name="reference" value="stool_small.unique.fasta"/>
132 <output name="vsearch.chimeras" ftype="txt"> 143 <output name="vsearch.chimeras" ftype="txt">
133 <assert_contents> 144 <assert_contents>