Mercurial > repos > iuc > mothur_remove_rare
comparison remove.rare.xml @ 3:39df13dda6bf draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
| author | iuc |
|---|---|
| date | Tue, 20 Mar 2018 21:57:22 -0400 |
| parents | c90c4b4a0fae |
| children | 189db1a23e9a |
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| 2:c90c4b4a0fae | 3:39df13dda6bf |
|---|---|
| 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 "$input.otu" input_otu.dat && | 13 ln -s '$input.otu' input_otu.dat && |
| 14 #if $input.source == 'list': | 14 #if $input.source == 'list': |
| 15 ln -s "$input.group" input.group.dat && | 15 ln -s '$input.group' input.group.dat && |
| 16 ln -s "$input.count" input.count.dat && | 16 ln -s '$input.count' input.count.dat && |
| 17 #end if | |
| 18 | |
| 19 echo 'remove.rare( | |
| 20 #if $input.otu.is_of_type("mothur.rabund"): | |
| 21 rabund=input_otu.dat, | |
| 22 #elif $input.otu.is_of_type("mothur.sabund"): | |
| 23 sabund=input_otu.dat, | |
| 24 #elif $input.otu.is_of_type("mothur.list"): | |
| 25 list=input_otu.dat, | |
| 26 #if $input.group: | |
| 27 group=input.group.dat, | |
| 17 #end if | 28 #end if |
| 18 | 29 #if $input.groups: |
| 19 echo 'remove.rare( | 30 groups=${ str($input.groups).replace(",","-") }, |
| 20 #if $input.otu.is_of_type("mothur.rabund"): | 31 #end if |
| 21 rabund=input_otu.dat, | 32 #if $input.count: |
| 22 #elif $input.otu.is_of_type("mothur.sabund"): | 33 count=input.count.dat, |
| 23 sabund=input_otu.dat, | 34 #end if |
| 24 #elif $input.otu.is_of_type("mothur.list"): | 35 #elif $input.otu.is_of_type("mothur.shared"): |
| 25 list=input_otu.dat, | 36 shared=input_otu.dat, |
| 26 #if $input.group: | 37 bygroup=$input.bygroup, |
| 27 group=input.group.dat, | 38 #if $input.groups: |
| 28 #end if | 39 groups=${ str($input.groups).replace(",","-") }, |
| 29 #if $input.groups: | 40 #end if |
| 30 groups=${ str($input.groups).replace(",","-") }, | 41 #end if |
| 31 #end if | 42 #if $input.label: |
| 32 #if $input.count: | 43 label=${ str($input.label).replace(",","-") }, |
| 33 count=input.count.dat, | 44 #end if |
| 34 #end if | 45 nseqs=$nseqs |
| 35 #elif $input.otu.is_of_type("mothur.shared"): | 46 )' |
| 36 shared=input_otu.dat, | 47 | sed 's/ //g' ## mothur trips over whitespace |
| 37 bygroup=$input.bygroup, | 48 | mothur |
| 38 #if $input.groups: | 49 | tee mothur.out.log |
| 39 groups=${ str($input.groups).replace(",","-") }, | |
| 40 #end if | |
| 41 #end if | |
| 42 #if $input.label: | |
| 43 label=${ str($input.label).replace(",","-") }, | |
| 44 #end if | |
| 45 nseqs=$nseqs | |
| 46 )' | |
| 47 | sed 's/ //g' ## mothur trips over whitespace | |
| 48 | mothur | |
| 49 | tee mothur.out.log | |
| 50 ]]></command> | 50 ]]></command> |
| 51 <inputs> | 51 <inputs> |
| 52 <conditional name="input"> | 52 <conditional name="input"> |
| 53 <param name="source" type="select" label="Select Input Format"> | 53 <param name="source" type="select" label="Select Input Format"> |
| 54 <option value="shared">shared</option> | 54 <option value="shared">shared</option> |
| 86 <expand macro="labeloptions"/> | 86 <expand macro="labeloptions"/> |
| 87 </param> | 87 </param> |
| 88 </when> | 88 </when> |
| 89 </conditional> | 89 </conditional> |
| 90 <param name="nseqs" type="integer" value="1" min="0" label="nseqs - Number of sequences cutoff for an otu to be deemed rare"/> | 90 <param name="nseqs" type="integer" value="1" min="0" label="nseqs - Number of sequences cutoff for an otu to be deemed rare"/> |
| 91 <expand macro="param-savelog"/> | |
| 91 </inputs> | 92 </inputs> |
| 92 <outputs> | 93 <outputs> |
| 93 <expand macro="logfile-output"/> | 94 <expand macro="logfile-output"/> |
| 94 <data name="pick_otu" format_source="otu" from_work_dir="input_otu*.pick.*" label="${tool.name} on ${on_string}: pick.${input.otu.ext}"> | 95 <data name="pick_otu" format_source="otu" from_work_dir="input_otu*.pick.*" label="${tool.name} on ${on_string}: pick.${input.otu.ext}"> |
| 95 <filter>input['source'] != 'shared'</filter> | 96 <filter>input['source'] != 'shared'</filter> |
| 105 <tests> | 106 <tests> |
| 106 <test><!-- test with list --> | 107 <test><!-- test with list --> |
| 107 <param name="source" value="list"/> | 108 <param name="source" value="list"/> |
| 108 <param name="otu" value="amazon.an.list" ftype="mothur.list"/> | 109 <param name="otu" value="amazon.an.list" ftype="mothur.list"/> |
| 109 <output name="pick_otu" md5="4779791c9b0ef95a54083ee1a6ad6c8d" ftype="mothur.list"/> | 110 <output name="pick_otu" md5="4779791c9b0ef95a54083ee1a6ad6c8d" ftype="mothur.list"/> |
| 111 <param name="savelog" value="true"/> | |
| 110 <expand macro="logfile-test"/> | 112 <expand macro="logfile-test"/> |
| 111 </test> | 113 </test> |
| 112 <test><!-- test with list and group file --> | 114 <test><!-- test with list and group file --> |
| 113 <param name="source" value="list"/> | 115 <param name="source" value="list"/> |
| 114 <param name="otu" value="amazon.an.list" ftype="mothur.list"/> | 116 <param name="otu" value="amazon.an.list" ftype="mothur.list"/> |
| 115 <param name="group" value="amazon.groups" ftype="mothur.groups"/> | 117 <param name="group" value="amazon.groups" ftype="mothur.groups"/> |
| 116 <param name="groups" value="forest,pasture"/> | 118 <param name="groups" value="forest,pasture"/> |
| 117 <output name="pick_otu" md5="4779791c9b0ef95a54083ee1a6ad6c8d" ftype="mothur.list"/> | 119 <output name="pick_otu" md5="4779791c9b0ef95a54083ee1a6ad6c8d" ftype="mothur.list"/> |
| 118 <output name="pick_group" md5="9561ba470c769670ab6d92563a44027f" ftype="mothur.groups"/> | 120 <output name="pick_group" md5="9561ba470c769670ab6d92563a44027f" ftype="mothur.groups"/> |
| 121 <param name="savelog" value="true"/> | |
| 119 <expand macro="logfile-test"/> | 122 <expand macro="logfile-test"/> |
| 120 </test> | 123 </test> |
| 121 <test><!-- test with shared file --> | 124 <test><!-- test with shared file --> |
| 122 <param name="source" value="shared"/> | 125 <param name="source" value="shared"/> |
| 123 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> | 126 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> |
| 124 <output_collection name="pick_shared" count="36"> | 127 <output_collection name="pick_shared" count="36"> |
| 125 <element name="0.38" md5="e58da633dd16f0cb6472d6c6b3318c9f" ftype="mothur.shared"/> | 128 <element name="0.38" md5="e58da633dd16f0cb6472d6c6b3318c9f" ftype="mothur.shared"/> |
| 126 </output_collection> | 129 </output_collection> |
| 130 <param name="savelog" value="true"/> | |
| 127 <expand macro="logfile-test"/> | 131 <expand macro="logfile-test"/> |
| 128 </test> | 132 </test> |
| 129 <test><!-- test with shared file and label/group select --> | 133 <test><!-- test with shared file and label/group select --> |
| 130 <param name="source" value="shared"/> | 134 <param name="source" value="shared"/> |
| 131 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> | 135 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> |
| 133 <param name="label" value="0.05,0.22,0.41"/> | 137 <param name="label" value="0.05,0.22,0.41"/> |
| 134 <param name="groups" value="forest,pasture"/> | 138 <param name="groups" value="forest,pasture"/> |
| 135 <output_collection name="pick_shared" count="3"> | 139 <output_collection name="pick_shared" count="3"> |
| 136 <element name="0.22" md5="46d97e6f97e7909d72d09a1726655539" ftype="mothur.shared"/> | 140 <element name="0.22" md5="46d97e6f97e7909d72d09a1726655539" ftype="mothur.shared"/> |
| 137 </output_collection> | 141 </output_collection> |
| 142 <param name="savelog" value="true"/> | |
| 138 <expand macro="logfile-test"/> | 143 <expand macro="logfile-test"/> |
| 139 </test> | 144 </test> |
| 140 <test><!-- test with rabund/sabund file --> | 145 <test><!-- test with rabund/sabund file --> |
| 141 <param name="source" value="default"/> | 146 <param name="source" value="default"/> |
| 142 <param name="otu" value="amazon.an.sabund" ftype="mothur.sabund"/> | 147 <param name="otu" value="amazon.an.sabund" ftype="mothur.sabund"/> |
| 143 <output name="pick_otu" md5="ca842ed3ef543d3dd76fd9089cd87c46" ftype="mothur.sabund"/> | 148 <output name="pick_otu" md5="ca842ed3ef543d3dd76fd9089cd87c46" ftype="mothur.sabund"/> |
| 149 <param name="savelog" value="true"/> | |
| 144 <expand macro="logfile-test"/> | 150 <expand macro="logfile-test"/> |
| 145 </test> | 151 </test> |
| 146 </tests> | 152 </tests> |
| 147 <help> | 153 <help><![CDATA[ |
| 148 <![CDATA[ | |
| 149 | 154 |
| 150 @MOTHUR_OVERVIEW@ | 155 @MOTHUR_OVERVIEW@ |
| 151 | 156 |
| 152 **Command Documentation** | 157 **Command Documentation** |
| 153 | 158 |
| 157 .. _sabund: https://www.mothur.org/wiki/Sabund_file | 162 .. _sabund: https://www.mothur.org/wiki/Sabund_file |
| 158 .. _rabund: https://www.mothur.org/wiki/Rabund_file | 163 .. _rabund: https://www.mothur.org/wiki/Rabund_file |
| 159 .. _shared: https://www.mothur.org/wiki/Shared_file | 164 .. _shared: https://www.mothur.org/wiki/Shared_file |
| 160 .. _remove.rare: https://www.mothur.org/wiki/Remove.rare | 165 .. _remove.rare: https://www.mothur.org/wiki/Remove.rare |
| 161 | 166 |
| 162 ]]> | 167 ]]></help> |
| 163 </help> | |
| 164 <expand macro="citations"/> | 168 <expand macro="citations"/> |
| 165 </tool> | 169 </tool> |