Mercurial > repos > iuc > mothur_align_check
diff align.check.xml @ 2:814a34469480 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
| author | iuc |
|---|---|
| date | Tue, 20 Mar 2018 22:14:06 -0400 |
| parents | 9d91e7974012 |
| children |
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--- a/align.check.xml Tue Sep 05 16:55:37 2017 -0400 +++ b/align.check.xml Tue Mar 20 22:14:06 2018 -0400 @@ -7,58 +7,67 @@ <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ - @SHELL_OPTIONS@ +@SHELL_OPTIONS@ - ## create symlinks to input datasets - ln -s "$fasta" fasta.dat && - ln -s "$name" name.dat && - ln -s "$count" count.dat && - ln -s "$map" map.dat && +## create symlinks to input datasets +ln -s '$fasta' fasta.dat && +ln -s '$name' name.dat && +ln -s '$count' count.dat && +ln -s '$map' map.dat && - echo 'align.check( - fasta=fasta.dat, - #if $name: - name=name.dat, - #end if - #if $count: - count=count.dat, - #end if - map=map.dat - )' - | sed 's/ //g' ## mothur trips over whitespace - | mothur - | tee mothur.out.log +echo 'align.check( + fasta=fasta.dat, + #if $name: + name=name.dat, + #end if + #if $count: + count=count.dat, + #end if + map=map.dat +)' +| sed 's/ //g' ## mothur trips over whitespace +| mothur +| tee mothur.out.log +&& cat fasta.align.check ]]></command> - <inputs> - <param name="fasta" type="data" format="mothur.align" label="fasta - Aligned Sequences"/> - <conditional name="ss"> - <param name="source" label="Select Secondary Structure Map from" type="select"> - <option value="cached">Cached Secondary Structure Maps</option> - <option value="history">Your History</option> + <inputs> + <param argument="fasta" type="data" format="mothur.align" label="fasta - Aligned Sequences"/> + <conditional name="ss"> + <param name="source" label="Select Secondary Structure Map from" type="select"> + <option value="cached">Cached Secondary Structure Maps</option> + <option value="history">Your History</option> + </param> + <when value="cached"> + <param argument="map" type="select" label="Secondary structure map"> + <options from_data_table="mothur_map"/> </param> - <when value="cached"> - <param name="map" type="select" label="map - Select a secondary structure map" help="Contact Galaxy team for additions"> - <options from_data_table="mothur_map"> - </options> - </param> - </when> - <when value="history"> - <param name="map" format="mothur.map" type="data" label="Secondary Structure Map"/> - </when> - </conditional> - <param name="count" type="data" format="mothur.count_table" label="count_table file" optional="true" help="You can also provide a name file associated with your fasta file"/> - <param name="name" type="data" format="mothur.names" label="names file" optional="true" help="The count file is similar to the name file in that it is used to represent the number of duplicate sequences for a given representative sequence"/> - </inputs> + </when> + <when value="history"> + <param argument="map" format="mothur.map" type="data" label="Secondary Structure Map"/> + </when> + </conditional> + <param argument="count" type="data" format="mothur.count_table" optional="true" label="count_table file" + help="You can also provide a name file associated with your fasta file"/> + <param argument="name" type="data" format="mothur.names" optional="true" label="names file" + help="The count file is similar to the name file in that it is used to represent the number of duplicate sequences for a given representative sequence"/> + <expand macro="param-savelog"/> + </inputs> <outputs> <expand macro="logfile-output"/> - <data name="out_file" format="mothur.align.check" from_work_dir="fasta.align.check" label="${tool.name} on ${on_string}: align.check"/> + <data name="align.check" format="mothur.align.check" from_work_dir="fasta.align.check" label="${tool.name} on ${on_string}: align.check"/> </outputs> <tests> <test><!-- test with defaults --> <param name="fasta" value="amazon.align_head_short"/> <param name="source" value="history"/> <param name="map" value="silva.ss.map.head"/> - <output name="out_file" md5="a785413dc157aacca4b19adef9cefa79" ftype="mothur.align.check"/> + <output name="align.check" ftype="mothur.align.check"> + <assert_contents> + <expand macro="test-aligncheck-format"/> + <has_text text="U68589"/> + </assert_contents> + </output> + <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> <test><!-- test with names file --> @@ -66,22 +75,29 @@ <param name="source" value="history"/> <param name="map" value="silva.ss.map.head"/> <param name="name" value="amazon.align_head.names"/> - <output name="out_file" md5="a785413dc157aacca4b19adef9cefa79" ftype="mothur.align.check"/> + <output name="align.check" ftype="mothur.align.check"> + <assert_contents> + <expand macro="test-aligncheck-format"/> + <has_text text="U68589"/> + </assert_contents> + </output> + <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> </tests> - <help> -<![CDATA[ + <help><![CDATA[ @MOTHUR_OVERVIEW@ **Command Documentation** -The align.check_ command allows you to calculate the number of potentially misaligned bases in a 16S rRNA gene sequence alignment using a secondary_structure_map_. If you are familiar with the editor window in ARB, this is the same as counting the number of ~, #, -, and = signs. +The align.check_ command allows you to calculate the number of potentially misaligned bases in a 16S rRNA gene sequence +alignment using a secondary_structure_map_. If you are familiar with the editor window in ARB, this is the same as +counting the number of ~, #, -, and = signs. .. _secondary_structure_map: https://www.mothur.org/wiki/Secondary_structure_map .. _align.check: https://www.mothur.org/wiki/Align.check -]]> - </help> + + ]]></help> <expand macro="citations"/> </tool>