Mercurial > repos > iuc > mothur_summary_single
comparison summary.single.xml @ 4:c4db2a4fdb42 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
| author | iuc |
|---|---|
| date | Wed, 14 Feb 2018 10:10:10 -0500 |
| parents | a92e6daa48d6 |
| children | ef3546864e3a |
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| 3:debe74cafeda | 4:c4db2a4fdb42 |
|---|---|
| 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 "$otu" otu.dat && | 13 ln -s '$otu' otu.dat && |
| 14 | 14 |
| 15 echo 'summary.single( | 15 echo 'summary.single( |
| 16 #if $otu.is_of_type("mothur.rabund"): | 16 #if $otu.is_of_type("mothur.rabund"): |
| 17 rabund=otu.dat | 17 rabund=otu.dat |
| 18 #elif $otu.is_of_type("mothur.sabund"): | 18 #elif $otu.is_of_type("mothur.sabund"): |
| 19 sabund=otu.dat | 19 sabund=otu.dat |
| 20 #elif $otu.is_of_type("mothur.list"): | 20 #elif $otu.is_of_type("mothur.list"): |
| 21 list=otu.dat | 21 list=otu.dat |
| 22 #elif $otu.is_of_type("mothur.shared"): | 22 #elif $otu.is_of_type("mothur.shared"): |
| 23 shared=otu.dat, | 23 shared=otu.dat, |
| 24 groupmode=$groupmode | 24 groupmode=$groupmode |
| 25 #end if | 25 #end if |
| 26 #if $label: | 26 #if $label: |
| 27 ,label=${ str($label).replace(",","-") } | 27 ,label=${ str($label).replace(",","-") } |
| 28 #end if | 28 #end if |
| 29 #if $calc: | 29 #if $calc: |
| 30 ,calc=${ str($calc).replace(",","-") } | 30 ,calc=${ str($calc).replace(",","-") } |
| 31 #end if | 31 #end if |
| 32 #if $abund: | 32 #if $abund: |
| 33 ,abund=$abund | 33 ,abund=$abund |
| 34 #end if | 34 #end if |
| 35 #if $size: | 35 #if $size: |
| 36 ,size=$size | 36 ,size=$size |
| 37 #end if | 37 #end if |
| 38 #if $subsample.use == 'yes': | 38 #if $subsample.use == 'yes': |
| 39 #if $subsample.subsample: | 39 #if $subsample.subsample: |
| 40 ,subsample=$subsample.subsample | 40 ,subsample=$subsample.subsample |
| 41 #else | 41 #else |
| 42 ,subsample=T | 42 ,subsample=T |
| 43 #end if | |
| 44 #if $subsample.iters: | |
| 45 ,iters=$subsample.iters | |
| 46 #end if | |
| 47 #end if | |
| 48 )' | |
| 49 | sed 's/ //g' ## mothur trips over whitespace | |
| 50 | mothur | |
| 51 | tee mothur.out.log | |
| 52 #if $subsample.use == 'yes' and not ($otu.extension == 'mothur.shared' and not $groupmode): | |
| 53 && mv otu.*ave-std.summary otu.ave-std | |
| 54 #end if | 43 #end if |
| 44 #if $subsample.iters: | |
| 45 ,iters=$subsample.iters | |
| 46 #end if | |
| 47 #end if | |
| 48 )' | |
| 49 | sed 's/ //g' ## mothur trips over whitespace | |
| 50 | mothur | |
| 51 | tee mothur.out.log | |
| 52 #if $subsample.use == 'yes' and not ($otu.extension == 'mothur.shared' and not $groupmode): | |
| 53 && mv otu.*ave_std.summary otu.ave-std | |
| 54 #end if | |
| 55 ]]></command> | 55 ]]></command> |
| 56 <inputs> | 56 <inputs> |
| 57 <param name="otu" type="data" format="mothur.list,mothur.rabund,mothur.sabund,mothur.shared" label="list,rabund,sabund,shared - OTU List"/> | 57 <param name="otu" type="data" format="mothur.list,mothur.rabund,mothur.sabund,mothur.shared" label="list,rabund,sabund,shared - OTU List"/> |
| 58 <param name="label" type="select" label="label - OTU Labels" multiple="true"> | 58 <param name="label" type="select" label="label - OTU Labels" multiple="true"> |
| 59 <expand macro="labeloptions"/> | 59 <expand macro="labeloptions"/> |
| 154 </assert_contents> | 154 </assert_contents> |
| 155 </output> | 155 </output> |
| 156 <expand macro="logfile-test"/> | 156 <expand macro="logfile-test"/> |
| 157 </test> | 157 </test> |
| 158 </tests> | 158 </tests> |
| 159 <help> | 159 <help><![CDATA[ |
| 160 <![CDATA[ | |
| 161 | 160 |
| 162 @MOTHUR_OVERVIEW@ | 161 @MOTHUR_OVERVIEW@ |
| 163 | 162 |
| 164 **Command Documentation** | 163 **Command Documentation** |
| 165 | 164 |
| 166 The summary.single_ command produce a summary file that has the calculator value for each line in the OTU data and for all possible comparisons between the different groups in the group_ file. This can be useful if you aren't interested in generating collector's or rarefaction curves for your multi-sample data analysis. It would be worth your while, however, to look at the collector's curves for the calculators you are interested in to determine how sensitive the values are to sampling. If the values are not sensitive to sampling, then you can trust the values. Otherwise, you need to keep sampling. For calc parameter choices see: https://www.mothur.org/wiki/Calculators | 165 The summary.single_ command produce a summary file that has the calculator value for each line in the OTU data and for all possible comparisons between the different groups in the group_ file. This can be useful if you aren't interested in generating collector's or rarefaction curves for your multi-sample data analysis. It would be worth your while, however, to look at the collector's curves for the calculators you are interested in to determine how sensitive the values are to sampling. If the values are not sensitive to sampling, then you can trust the values. Otherwise, you need to keep sampling. For calc parameter choices see: https://www.mothur.org/wiki/Calculators |
| 167 | 166 |
| 168 .. _group: https://www.mothur.org/wiki/Group_file | 167 .. _group: https://www.mothur.org/wiki/Group_file |
| 169 .. _summary.single: https://www.mothur.org/wiki/Summary.single | 168 .. _summary.single: https://www.mothur.org/wiki/Summary.single |
| 170 ]]> | 169 |
| 171 </help> | 170 ]]></help> |
| 172 <expand macro="citations"/> | 171 <expand macro="citations"/> |
| 173 </tool> | 172 </tool> |