Mercurial > repos > iuc > mothur_summary_tax
comparison summary.tax.xml @ 2:f7dded265782 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
| author | iuc |
|---|---|
| date | Tue, 20 Mar 2018 22:24:38 -0400 |
| parents | 76c27b0fa016 |
| children |
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| 1:807ebe300c84 | 2:f7dded265782 |
|---|---|
| 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 "$tax.taxonomy" tax.taxonomy.dat && | 13 ln -s '$tax.taxonomy' tax.taxonomy.dat && |
| 14 ln -s "$name" name.dat && | 14 ln -s '$name' name.dat && |
| 15 ln -s "$group" group.dat && | 15 ln -s '$group' group.dat && |
| 16 ln -s "$count" count.dat && | 16 ln -s '$count' count.dat && |
| 17 #if $reftax.source2: | |
| 18 ln -s "$reftax.reftaxonomy" myreftax.taxonomy && | |
| 19 ln -s "$sum" myreftax.tree.sum && | |
| 20 #end if | |
| 21 | 17 |
| 22 echo 'summary.tax( | 18 echo 'summary.tax( |
| 23 taxonomy=tax.taxonomy.dat, | 19 taxonomy=tax.taxonomy.dat, |
| 24 #if $name: | 20 #if $name: |
| 25 name=name.dat, | 21 name=name.dat, |
| 26 #end if | 22 #end if |
| 27 #if $group: | 23 #if $group: |
| 28 group=group.dat, | 24 group=group.dat, |
| 29 #end if | 25 #end if |
| 30 #if $reftax.source2: | 26 #if $count: |
| 31 reftaxonomy=myreftax.taxonomy, | 27 count=count.dat, |
| 32 #end if | 28 #end if |
| 33 #if $count: | 29 relabund=$relabund, |
| 34 count=count.dat, | 30 threshold=$threshold, |
| 35 #end if | 31 output=$output, |
| 36 relabund=$relabund | 32 printlevel=$printlevel |
| 37 )' | 33 )' |
| 38 | sed 's/ //g' ## mothur trips over whitespace | 34 | sed 's/ //g' ## mothur trips over whitespace |
| 39 | mothur | 35 | mothur |
| 40 | tee mothur.out.log | 36 | tee mothur.out.log |
| 41 ]]></command> | 37 ]]></command> |
| 42 <inputs> | 38 <inputs> |
| 43 <conditional name="tax"> | 39 <conditional name="tax"> |
| 44 <param name="source" type="select" label="Select Taxonomy from" help=""> | 40 <param name="source" type="select" label="Select Taxonomy from" help=""> |
| 45 <option value="hist">History</option> | 41 <option value="hist">History</option> |
| 54 <param name="taxonomy" type="data" format="mothur.seq.taxonomy" label="taxonomy - Taxonomy Reference"/> | 50 <param name="taxonomy" type="data" format="mothur.seq.taxonomy" label="taxonomy - Taxonomy Reference"/> |
| 55 </when> | 51 </when> |
| 56 </conditional> | 52 </conditional> |
| 57 <param name="name" type="data" format="mothur.names" optional="true" label="name - taxonomy sequence names"/> | 53 <param name="name" type="data" format="mothur.names" optional="true" label="name - taxonomy sequence names"/> |
| 58 <param name="group" type="data" format="mothur.groups" optional="true" label="group - Groups for summary file"/> | 54 <param name="group" type="data" format="mothur.groups" optional="true" label="group - Groups for summary file"/> |
| 59 <conditional name="reftax"> | |
| 60 <param name="source2" type="select" label="Select Reference Taxonomy used in Summary.seqs from" help="Including the reference taxonomy file used when you classified your sequences keep the rankIDs in the summary file static."> | |
| 61 <option value="" selected="true">Selection is Optional</option> | |
| 62 <option value="hist">History</option> | |
| 63 <option value="ref">Cached Reference</option> | |
| 64 </param> | |
| 65 <when value="ref"> | |
| 66 <param name="reftaxonomy" type="select" format="mothur.seq.taxonomy" label="reftaxonomy - Taxonomy Reference used when sequences were classified"> | |
| 67 <options from_data_table="mothur_taxonomy"/> | |
| 68 </param> | |
| 69 <param name="sum" type="data" format="tabular" label="tree.sum - summary file produced when sequences were classified" help="run classify.seqs to get this file"/> | |
| 70 </when> | |
| 71 <when value="hist"> | |
| 72 <param name="reftaxonomy" type="data" format="mothur.seq.taxonomy" label="reftaxonomy - Taxonomy Reference used when sequences were classified"/> | |
| 73 <param name="sum" type="data" format="tabular" label="tree.sum - summary file produced when sequences were classified" help="run classify.seqs to get this file"/> | |
| 74 </when> | |
| 75 <when value=""/> | |
| 76 </conditional> | |
| 77 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/> | 55 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/> |
| 78 <param name="relabund" type="boolean" falsevalue="false" truevalue="true" checked="false" label="relabund - allows you to indicate that you want the summary files to be relative abundances rather than raw abundances. default=f"/> | 56 <param name="relabund" type="boolean" falsevalue="false" truevalue="true" checked="false" |
| 57 label="relabund - allows you to indicate that you want the summary files to be relative abundances rather than raw abundances. default=f"/> | |
| 58 <param name="threshold" type="integer" value="0" min="0" label="threshold- specify a cutoff for the taxonomy file" | |
| 59 help="Once the classification falls below the threshold the mothur will refer to it as unclassified when calculating the concensus. | |
| 60 This feature is similar to adjusting the cutoff in classify.seqs"/> | |
| 61 <expand macro="param-output"/> | |
| 62 <expand macro="param-printlevel"/> | |
| 63 <expand macro="param-savelog"/> | |
| 79 </inputs> | 64 </inputs> |
| 80 <outputs> | 65 <outputs> |
| 81 <expand macro="logfile-output"/> | 66 <expand macro="logfile-output"/> |
| 82 <data name="taxsummary" format="mothur.summary" from_work_dir="tax.taxonomy*.tax.summary" label="${tool.name} on ${on_string}: summary"/> | 67 <data name="taxsummary" format="mothur.tax.summary" from_work_dir="tax.taxonomy*.tax.summary" label="${tool.name} on ${on_string}: summary"/> |
| 83 </outputs> | 68 </outputs> |
| 84 <tests> | 69 <tests> |
| 85 <test> | 70 <test> |
| 86 <param name="source" value="hist"/> | 71 <param name="source" value="hist"/> |
| 87 <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/> | 72 <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/> |
| 88 <output name="taxsummary" md5="1019aae0e68b2ee102565c535a8e03cf" ftype="mothur.summary"/> | 73 <output name="taxsummary" ftype="mothur.tax.summary"> |
| 74 <assert_contents> | |
| 75 <expand macro="test-taxsummary-format"/> | |
| 76 <has_text text="Root"/> | |
| 77 <has_text text="Bifidobacterium"/> | |
| 78 </assert_contents> | |
| 79 </output> | |
| 80 <param name="savelog" value="true"/> | |
| 89 <expand macro="logfile-test"/> | 81 <expand macro="logfile-test"/> |
| 90 </test> | 82 </test> |
| 91 <test> | 83 <test> |
| 92 <param name="source" value="hist"/> | 84 <param name="source" value="hist"/> |
| 93 <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/> | 85 <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/> |
| 94 <param name="source2" value="hist"/> | 86 <output name="taxsummary" ftype="mothur.tax.summary"> |
| 95 <param name="reftaxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/> | 87 <assert_contents> |
| 96 <param name="sum" value="abrecovery.pds.wang.tree.sum"/> | 88 <expand macro="test-taxsummary-format"/> |
| 97 <output name="taxsummary" md5="1019aae0e68b2ee102565c535a8e03cf" ftype="mothur.summary"/> | 89 <has_text text="Root"/> |
| 90 <has_text text="Bifidobacterium"/> | |
| 91 </assert_contents> | |
| 92 </output> | |
| 93 <param name="savelog" value="true"/> | |
| 98 <expand macro="logfile-test"/> | 94 <expand macro="logfile-test"/> |
| 99 </test> | 95 </test> |
| 100 </tests> | 96 </tests> |
| 101 <help> | 97 <help><![CDATA[ |
| 102 <![CDATA[ | |
| 103 | 98 |
| 104 @MOTHUR_OVERVIEW@ | 99 @MOTHUR_OVERVIEW@ |
| 105 | 100 |
| 106 **Command Documentation** | 101 **Command Documentation** |
| 107 | 102 |
| 108 The summary.tax_ command reads a taxonomy file and an optional name and or group file, and summarizes the taxonomy information. | 103 The summary.tax_ command reads a taxonomy file and an optional name and or group file, and summarizes the taxonomy information. |
| 109 | 104 |
| 110 .. _summary.tax: https://www.mothur.org/wiki/Summary.tax | 105 .. _summary.tax: https://www.mothur.org/wiki/Summary.tax |
| 111 ]]> | 106 |
| 112 </help> | 107 ]]></help> |
| 113 <expand macro="citations"/> | 108 <expand macro="citations"/> |
| 114 </tool> | 109 </tool> |