Mercurial > repos > iuc > mothur_get_seqs
comparison get.seqs.xml @ 5:130711597b24 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 38a2bbee32eaaceeb22d7549b13dbc0c613ee173
| author | iuc |
|---|---|
| date | Tue, 20 Mar 2018 13:32:52 -0400 |
| parents | ef6de2793ab6 |
| children |
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| 4:c4cf325443ee | 5:130711597b24 |
|---|---|
| 66 <param name="group_in" type="data" format="mothur.groups" optional="true" label="group - Sequences Groups"/> | 66 <param name="group_in" type="data" format="mothur.groups" optional="true" label="group - Sequences Groups"/> |
| 67 <param name="alignreport_in" type="data" format="mothur.align.report" optional="true" label="alignreport - Align Report"/> | 67 <param name="alignreport_in" type="data" format="mothur.align.report" optional="true" label="alignreport - Align Report"/> |
| 68 <param name="list_in" type="data" format="mothur.list" optional="true" label="list - OTU List"/> | 68 <param name="list_in" type="data" format="mothur.list" optional="true" label="list - OTU List"/> |
| 69 <param name="taxonomy_in" type="data" format="mothur.seq.taxonomy" optional="true" label="taxonomy - Taxonomy"/> | 69 <param name="taxonomy_in" type="data" format="mothur.seq.taxonomy" optional="true" label="taxonomy - Taxonomy"/> |
| 70 <param name="dups" type="boolean" truevalue="dups" falsevalue="false" checked="true" label="dups - Apply to duplicates"/> | 70 <param name="dups" type="boolean" truevalue="dups" falsevalue="false" checked="true" label="dups - Apply to duplicates"/> |
| 71 <expand macro="param-savelog"/> | |
| 71 </inputs> | 72 </inputs> |
| 72 <outputs> | 73 <outputs> |
| 73 <expand macro="logfile-output"/> | 74 <expand macro="logfile-output"/> |
| 74 <data name="fasta_out" format_source="fasta_in" from_work_dir="fasta_in*.pick.*" label="${tool.name} on ${on_string}: pick.fasta"> | 75 <data name="fasta_out" format_source="fasta_in" from_work_dir="fasta_in*.pick.*" label="${tool.name} on ${on_string}: pick.fasta"> |
| 75 <filter>fasta_in</filter> | 76 <filter>fasta_in</filter> |
| 103 <test> | 104 <test> |
| 104 <param name="accnos" value="Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos"/> | 105 <param name="accnos" value="Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos"/> |
| 105 <param name="fasta_in" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta"/> | 106 <param name="fasta_in" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta"/> |
| 106 <param name="dups" value=""/> | 107 <param name="dups" value=""/> |
| 107 <output name="fasta_out" md5="f9335b6b70dc639e420d33809e51431d"/> | 108 <output name="fasta_out" md5="f9335b6b70dc639e420d33809e51431d"/> |
| 109 <param name="savelog" value="true"/> | |
| 108 <expand macro="logfile-test"/> | 110 <expand macro="logfile-test"/> |
| 109 </test> | 111 </test> |
| 110 <test> | 112 <test> |
| 111 <param name="accnos" value="Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos"/> | 113 <param name="accnos" value="Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos"/> |
| 112 <param name="fastq_in" value="Mock_S280_L001_R1_001_small.fastq"/> | 114 <param name="fastq_in" value="Mock_S280_L001_R1_001_small.fastq"/> |
| 113 <output name="fastq_out" md5="81d026f969e15b8c8701f8dc5f3a6904"/> | 115 <output name="fastq_out" md5="81d026f969e15b8c8701f8dc5f3a6904"/> |
| 116 <param name="savelog" value="true"/> | |
| 114 <expand macro="logfile-test"/> | 117 <expand macro="logfile-test"/> |
| 115 </test> | 118 </test> |
| 116 <test> | 119 <test> |
| 117 <!-- test two input files --> | 120 <!-- test two input files --> |
| 118 <param name="accnos" value="Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos"/> | 121 <param name="accnos" value="Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos"/> |
| 119 <param name="fasta_in" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta"/> | 122 <param name="fasta_in" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta"/> |
| 120 <param name="fastq_in" value="Mock_S280_L001_R1_001_small.fastq"/> | 123 <param name="fastq_in" value="Mock_S280_L001_R1_001_small.fastq"/> |
| 121 <param name="dups" value="false"/> | 124 <param name="dups" value="false"/> |
| 122 <output name="fasta_out" md5="f9335b6b70dc639e420d33809e51431d"/> | 125 <output name="fasta_out" md5="f9335b6b70dc639e420d33809e51431d"/> |
| 123 <output name="fastq_out" md5="81d026f969e15b8c8701f8dc5f3a6904"/> | 126 <output name="fastq_out" md5="81d026f969e15b8c8701f8dc5f3a6904"/> |
| 127 <param name="savelog" value="true"/> | |
| 124 <expand macro="logfile-test"/> | 128 <expand macro="logfile-test"/> |
| 125 </test> | 129 </test> |
| 126 <test> | 130 <test> |
| 127 <param name="accnos" value="amazon.bad.accnos"/> | 131 <param name="accnos" value="amazon.bad.accnos"/> |
| 128 <param name="count_in" value="amazon.count_table"/> | 132 <param name="count_in" value="amazon.count_table"/> |
| 129 <output name="count_out" md5="6892dd99850ce9e9f8f15e77b28f57e2"/> | 133 <output name="count_out" md5="6892dd99850ce9e9f8f15e77b28f57e2"/> |
| 134 <param name="savelog" value="true"/> | |
| 130 <expand macro="logfile-test"/> | 135 <expand macro="logfile-test"/> |
| 131 </test> | 136 </test> |
| 132 </tests> | 137 </tests> |
| 133 <help><![CDATA[ | 138 <help><![CDATA[ |
| 134 | 139 |