Mercurial > repos > iuc > mothur_get_seqs
comparison get.seqs.xml @ 2:5acd4d7339b9 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
| author | iuc |
|---|---|
| date | Tue, 20 Mar 2018 21:55:58 -0400 |
| parents | bfd467665e6c |
| children | c8b640a7aea1 |
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| 1:9cefa4fac685 | 2:5acd4d7339b9 |
|---|---|
| 5 </macros> | 5 </macros> |
| 6 <expand macro="requirements"/> | 6 <expand macro="requirements"/> |
| 7 <expand macro="stdio"/> | 7 <expand macro="stdio"/> |
| 8 <expand macro="version_command"/> | 8 <expand macro="version_command"/> |
| 9 <command><![CDATA[ | 9 <command><![CDATA[ |
| 10 @SHELL_OPTIONS@ | 10 @SHELL_OPTIONS@ |
| 11 | 11 |
| 12 ## create symlinks to input datasets | 12 ## create symlinks to input datasets |
| 13 ln -s "$accnos" accnos.dat && | 13 ln -s '$accnos' accnos.dat && |
| 14 ln -s "$fasta_in" fasta_in.dat && | 14 ln -s '$fasta_in' fasta_in.dat && |
| 15 ln -s "$fastq_in" fastq_in.dat && | 15 ln -s '$fastq_in' fastq_in.dat && |
| 16 ln -s "$count_in" count_in.dat && | 16 ln -s '$count_in' count_in.dat && |
| 17 ln -s "$qfile_in" qfile_in.dat && | 17 ln -s '$qfile_in' qfile_in.dat && |
| 18 ln -s "$name_in" name_in.dat && | 18 ln -s '$name_in' name_in.dat && |
| 19 ln -s "$group_in" group_in.dat && | 19 ln -s '$group_in' group_in.dat && |
| 20 ln -s "$alignreport_in" alignreport_in.dat && | 20 ln -s '$alignreport_in' alignreport_in.dat && |
| 21 ln -s "$list_in" list_in.dat && | 21 ln -s '$list_in' list_in.dat && |
| 22 ln -s "$taxonomy_in" taxonomy_in.dat && | 22 ln -s '$taxonomy_in' taxonomy_in.dat && |
| 23 | 23 |
| 24 echo 'get.seqs( | 24 echo 'get.seqs( |
| 25 accnos=accnos.dat, | 25 accnos=accnos.dat, |
| 26 #if $fasta_in: | 26 #if $fasta_in: |
| 27 fasta=fasta_in.dat, | 27 fasta=fasta_in.dat, |
| 28 #end if | 28 #end if |
| 29 #if $fastq_in: | 29 #if $fastq_in: |
| 30 fastq=fastq_in.dat, | 30 fastq=fastq_in.dat, |
| 31 #end if | 31 #end if |
| 32 #if $count_in: | 32 #if $count_in: |
| 33 count=count_in.dat, | 33 count=count_in.dat, |
| 34 #end if | 34 #end if |
| 35 #if $qfile_in: | 35 #if $qfile_in: |
| 36 qfile=qfile_in.dat, | 36 qfile=qfile_in.dat, |
| 37 #end if | 37 #end if |
| 38 #if $name_in: | 38 #if $name_in: |
| 39 name=name_in.dat, | 39 name=name_in.dat, |
| 40 #end if | 40 #end if |
| 41 #if $group_in: | 41 #if $group_in: |
| 42 group=group_in.dat, | 42 group=group_in.dat, |
| 43 #end if | 43 #end if |
| 44 #if $alignreport_in: | 44 #if $alignreport_in: |
| 45 alignreport=alignreport_in.dat, | 45 alignreport=alignreport_in.dat, |
| 46 #end if | 46 #end if |
| 47 #if $list_in: | 47 #if $list_in: |
| 48 list=list_in.dat, | 48 list=list_in.dat, |
| 49 #end if | 49 #end if |
| 50 #if $taxonomy_in: | 50 #if $taxonomy_in: |
| 51 taxonomy=taxonomy_in.dat, | 51 taxonomy=taxonomy_in.dat, |
| 52 #end if | 52 #end if |
| 53 dups=$dups | 53 dups=$dups |
| 54 )' | 54 )' |
| 55 | sed 's/ //g' ## mothur trips over whitespace | 55 | sed 's/ //g' ## mothur trips over whitespace |
| 56 | mothur | 56 | mothur |
| 57 | tee mothur.out.log | 57 | tee mothur.out.log |
| 58 ]]></command> | 58 ]]></command> |
| 59 <inputs> | 59 <inputs> |
| 60 <param name="accnos" type="data" format="mothur.accnos" label="accnos - Accession Names"/> | 60 <param name="accnos" type="data" format="mothur.accnos" label="accnos - Accession Names"/> |
| 61 <param name="fasta_in" type="data" format="fasta" optional="true" label="fasta - Fasta Sequences"/> | 61 <param name="fasta_in" type="data" format="fasta" optional="true" label="fasta - Fasta Sequences"/> |
| 62 <param name="qfile_in" type="data" format="qual" optional="true" label="qfile - Fasta Quality"/> | 62 <param name="qfile_in" type="data" format="qual" optional="true" label="qfile - Fasta Quality"/> |
| 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="e9aae546bf9c00cb7e884dff267d4ba1"/> | 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="e9aae546bf9c00cb7e884dff267d4ba1"/> | 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> | 138 <help><![CDATA[ |
| 134 <![CDATA[ | |
| 135 | 139 |
| 136 @MOTHUR_OVERVIEW@ | 140 @MOTHUR_OVERVIEW@ |
| 137 | 141 |
| 138 **Command Documentation** | 142 **Command Documentation** |
| 139 | 143 |
| 146 .. _taxonomy: https://www.mothur.org/wiki/Taxonomy_outline | 150 .. _taxonomy: https://www.mothur.org/wiki/Taxonomy_outline |
| 147 .. _list.seqs: https://www.mothur.org/wiki/list.seqs | 151 .. _list.seqs: https://www.mothur.org/wiki/list.seqs |
| 148 .. _get.seqs: https://www.mothur.org/wiki/Get.seqs | 152 .. _get.seqs: https://www.mothur.org/wiki/Get.seqs |
| 149 | 153 |
| 150 v.1.27.0 : Updated to Mothur 1.33, added count and fastq params | 154 v.1.27.0 : Updated to Mothur 1.33, added count and fastq params |
| 151 ]]> | 155 |
| 152 </help> | 156 ]]></help> |
| 153 <expand macro="citations"/> | 157 <expand macro="citations"/> |
| 154 </tool> | 158 </tool> |