Mercurial > repos > iuc > meryl
diff meryl.xml @ 6:31fa26c0692b draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 719ee1a23c0177886977f519f03c4032b97260b3"
author | iuc |
---|---|
date | Tue, 08 Jun 2021 07:20:29 +0000 |
parents | d63739222f68 |
children | 51c2360aa807 |
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--- a/meryl.xml Sun May 23 18:09:41 2021 +0000 +++ b/meryl.xml Tue Jun 08 07:20:29 2021 +0000 @@ -49,16 +49,12 @@ output read-db.meryl && tar -zcf read-db.meryldb read-db.meryl #elif $operation_type.command_type == 'groups-kmers' - mkdir -p ./temp_db/ && - tar -zxf $operation_type.input_meryldb_02 -C ./temp_db/ && - mv ./temp_db/* tmp_01.meryl && - tar -zxf $operation_type.input_meryldb_03 -C ./temp_db/ && - mv ./temp_db/* tmp_02.meryl && - meryl - $operation_type.groups_operations - tmp_01.meryl - tmp_02.meryl - output read-db.meryl && + #for $i,$mdb in enumerate($operation_type.input_meryldb_02) + mkdir -p ./tmp_folder_$i/ && + tar -zxf $mdb -C ./tmp_folder_$i && + mv ./tmp_folder_$i/* db_'${i}'.meryl && + #end for + meryl $operation_type.groups_operations output read-db.meryl db_* && tar -zcf read-db.meryldb read-db.meryl #elif $operation_type.command_type == 'histogram-kmers' mkdir -p ./temp_db/ && @@ -220,8 +216,7 @@ <option value="difference">Difference: return k-mers that occur in the first input, but none of the other inputs</option> <option value="symmetric-difference">Symmetric-difference: return k-mers that occur in exactly one input</option> </param> - <param name="input_meryldb_02" type="data" format="meryldb" label="Input meryldb" /> - <param name="input_meryldb_03" type="data" format="meryldb" label="Input meryldb" /> + <param name="input_meryldb_02" type="data" multiple="true" format="meryldb" label="Input meryldb" /> </when> <when value="histogram-kmers"> <param name="input_meryldb_02" type="data" format="meryldb" label="Input meryldb" /> @@ -450,8 +445,8 @@ <conditional name="operation_type"> <param name="command_type" value="groups-kmers" /> <param name="groups_operations" value="union" /> - <param name="input_meryldb_02" value="output_02.read-db.meryldb" ftype="meryldb" /> - <param name="input_meryldb_03" value="output_03.read-db.meryldb" ftype="meryldb" /> + <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb" /> + <param name="input_meryldb_03" value="" ftype="meryldb" /> </conditional> <output name="read_db" ftype="meryldb"> <assert_contents> @@ -463,8 +458,7 @@ <conditional name="operation_type"> <param name="command_type" value="groups-kmers" /> <param name="groups_operations" value="union-min" /> - <param name="input_meryldb_02" value="output_02.read-db.meryldb" ftype="meryldb" /> - <param name="input_meryldb_03" value="output_03.read-db.meryldb" ftype="meryldb" /> + <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb" /> </conditional> <output name="read_db" ftype="meryldb"> <assert_contents> @@ -476,8 +470,7 @@ <conditional name="operation_type"> <param name="command_type" value="groups-kmers" /> <param name="groups_operations" value="union-max" /> - <param name="input_meryldb_02" value="output_02.read-db.meryldb" ftype="meryldb" /> - <param name="input_meryldb_03" value="output_03.read-db.meryldb" ftype="meryldb" /> + <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb" /> </conditional> <output name="read_db" ftype="meryldb"> <assert_contents> @@ -489,8 +482,7 @@ <conditional name="operation_type"> <param name="command_type" value="groups-kmers" /> <param name="groups_operations" value="union-sum" /> - <param name="input_meryldb_02" value="output_02.read-db.meryldb" ftype="meryldb" /> - <param name="input_meryldb_03" value="output_03.read-db.meryldb" ftype="meryldb" /> + <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb" /> </conditional> <output name="read_db" ftype="meryldb"> <assert_contents> @@ -502,8 +494,7 @@ <conditional name="operation_type"> <param name="command_type" value="groups-kmers" /> <param name="groups_operations" value="intersect" /> - <param name="input_meryldb_02" value="output_02.read-db.meryldb" ftype="meryldb" /> - <param name="input_meryldb_03" value="output_03.read-db.meryldb" ftype="meryldb" /> + <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb" /> </conditional> <output name="read_db" ftype="meryldb"> <assert_contents> @@ -515,8 +506,7 @@ <conditional name="operation_type"> <param name="command_type" value="groups-kmers" /> <param name="groups_operations" value="intersect-min" /> - <param name="input_meryldb_02" value="output_02.read-db.meryldb" ftype="meryldb" /> - <param name="input_meryldb_03" value="output_03.read-db.meryldb" ftype="meryldb" /> + <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb" /> </conditional> <output name="read_db" ftype="meryldb"> <assert_contents> @@ -528,8 +518,7 @@ <conditional name="operation_type"> <param name="command_type" value="groups-kmers" /> <param name="groups_operations" value="intersect-max" /> - <param name="input_meryldb_02" value="output_02.read-db.meryldb" ftype="meryldb" /> - <param name="input_meryldb_03" value="output_03.read-db.meryldb" ftype="meryldb" /> + <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb" /> </conditional> <output name="read_db" ftype="meryldb"> <assert_contents> @@ -541,8 +530,7 @@ <conditional name="operation_type"> <param name="command_type" value="groups-kmers" /> <param name="groups_operations" value="intersect-sum" /> - <param name="input_meryldb_02" value="output_02.read-db.meryldb" ftype="meryldb" /> - <param name="input_meryldb_03" value="output_03.read-db.meryldb" ftype="meryldb" /> + <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb" /> </conditional> <output name="read_db" ftype="meryldb"> <assert_contents> @@ -555,8 +543,7 @@ <conditional name="operation_type"> <param name="command_type" value="groups-kmers" /> <param name="groups_operations" value="subtract" /> - <param name="input_meryldb_02" value="output_02.read-db.meryldb" ftype="meryldb" /> - <param name="input_meryldb_03" value="output_03.read-db.meryldb" ftype="meryldb" /> + <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb" /> </conditional> <output name="read_db" ftype="meryldb"> <assert_contents> @@ -568,8 +555,7 @@ <conditional name="operation_type"> <param name="command_type" value="groups-kmers" /> <param name="groups_operations" value="difference" /> - <param name="input_meryldb_02" value="output_02.read-db.meryldb" ftype="meryldb" /> - <param name="input_meryldb_03" value="output_03.read-db.meryldb" ftype="meryldb" /> + <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb" /> </conditional> <output name="read_db" ftype="meryldb"> <assert_contents> @@ -581,8 +567,7 @@ <conditional name="operation_type"> <param name="command_type" value="groups-kmers" /> <param name="groups_operations" value="symmetric-difference" /> - <param name="input_meryldb_02" value="output_02.read-db.meryldb" ftype="meryldb" /> - <param name="input_meryldb_03" value="output_03.read-db.meryldb" ftype="meryldb" /> + <param name="input_meryldb_02" value="output_02.read-db.meryldb,output_03.read-db.meryldb" ftype="meryldb" /> </conditional> <output name="read_db" ftype="meryldb"> <assert_contents>