Mercurial > repos > iuc > mothur_make_group
changeset 4:63a75db03ecc draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit be5c8af076296a53959fc3ed2b82d92dc7607eeb
| author | iuc |
|---|---|
| date | Mon, 23 Apr 2018 09:42:15 -0400 |
| parents | 43f7c6cfc023 |
| children | afc13b55ead3 |
| files | make.group.xml test-data/make_group_collection.groups |
| diffstat | 2 files changed, 40 insertions(+), 4 deletions(-) [+] |
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--- a/make.group.xml Fri Apr 06 04:13:02 2018 -0400 +++ b/make.group.xml Mon Apr 23 09:42:15 2018 -0400 @@ -9,15 +9,18 @@ <command><![CDATA[ @SHELL_OPTIONS@ +#import re + #set fastas = '' #set groups = '' #set count = 0 #if $method.how == 'collection': #for $i in $method.fasta_collection: - ln -s '$i' fasta_${i.element_identifier}.dat && - #set fastas+='fasta_'+$i.element_identifier+'.dat-' - #set groups+=$i.element_identifier+'-' + #set $identifier=re.sub('[^\w_]', '_', str($i.element_identifier)) + ln -s '$i' 'fasta_${identifier}.dat' && + #set fastas+='fasta_'+$identifier+'.dat-' + #set groups+=$identifier+'-' #end for #else #for $i in $method.inputs: @@ -43,7 +46,8 @@ <option value="manually"> Manually specify fasta files and group names</option> </param> <when value="collection"> - <param name="fasta_collection" type="data_collection" collection_type="list" format="fasta" label="Collection with fasta files to group" help="group names will be named after the collection element names"/> + <param name="fasta_collection" type="data_collection" collection_type="list" format="fasta" label="Collection with fasta files to group" + help="group names will be derived from the dataset names of the collection elements, please make sure these are meaningful names"/> </when> <when value="manually"> <repeat name="inputs" title="Additional"> @@ -85,6 +89,18 @@ <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> + <test> <!-- test with spaces or hyphens in element identifier --> + <param name="how" value="collection"/> + <param name="fasta_collection"> + <collection type="list"> + <element name="test group" ftype="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head" /> + <element name="test-group2" ftype="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head" /> + </collection> + </param> + <output name="output" file="make_group_collection.groups"/> + <param name="savelog" value="true"/> + <expand macro="logfile-test"/> + </test> </tests> <help><![CDATA[
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/make_group_collection.groups Mon Apr 23 09:42:15 2018 -0400 @@ -0,0 +1,20 @@ +M00967_43_000000000-A3JHG_1_1101_19936_3208 test_group +M00967_43_000000000-A3JHG_1_1101_15923_3823 test_group +M00967_43_000000000-A3JHG_1_1101_14010_4122 test_group +M00967_43_000000000-A3JHG_1_1101_13293_4703 test_group +M00967_43_000000000-A3JHG_1_1101_24357_4866 test_group +M00967_43_000000000-A3JHG_1_1101_23552_5194 test_group +M00967_43_000000000-A3JHG_1_1101_7326_5417 test_group +M00967_43_000000000-A3JHG_1_1101_11148_6457 test_group +M00967_43_000000000-A3JHG_1_1101_7079_6722 test_group +M00967_43_000000000-A3JHG_1_1101_8607_6805 test_group +M00967_43_000000000-A3JHG_1_1101_19936_3208 test_group2 +M00967_43_000000000-A3JHG_1_1101_15923_3823 test_group2 +M00967_43_000000000-A3JHG_1_1101_14010_4122 test_group2 +M00967_43_000000000-A3JHG_1_1101_13293_4703 test_group2 +M00967_43_000000000-A3JHG_1_1101_24357_4866 test_group2 +M00967_43_000000000-A3JHG_1_1101_23552_5194 test_group2 +M00967_43_000000000-A3JHG_1_1101_7326_5417 test_group2 +M00967_43_000000000-A3JHG_1_1101_11148_6457 test_group2 +M00967_43_000000000-A3JHG_1_1101_7079_6722 test_group2 +M00967_43_000000000-A3JHG_1_1101_8607_6805 test_group2