Mercurial > repos > matnguyen > pathogist
comparison galaxy/tools/concatenator/concatenator.xml @ 2:baf1e89b42eb draft
Added config builder
| author | matnguyen |
|---|---|
| date | Tue, 05 Mar 2019 02:36:40 -0500 |
| parents | c1b6f5fbbcad |
| children | a39471bf7d13 |
comparison
equal
deleted
inserted
replaced
| 1:c1b6f5fbbcad | 2:baf1e89b42eb |
|---|---|
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="package" version="0.2.3">pathogist</requirement> | 4 <requirement type="package" version="0.2.3">pathogist</requirement> |
| 5 </requirements> | 5 </requirements> |
| 6 | 6 |
| 7 <command><![CDATA[ | 7 <command><![CDATA[ |
| 8 $__tool_directory__/concatenator -n #for $path in $paths# ${path.element_identifier} #end for# | 8 $__tool_directory__/concatenator |
| 9 -i #for $path in $paths# $path #end for# | 9 |
| 10 #if $input_type.input_type_selector == "variant" | |
| 11 variant | |
| 12 -n #for $path in $input_type.paths# ${path.element_identifier} #end for# | |
| 13 -i #for $path in $input_type.paths# $path #end for# | |
| 14 #elif $input_type.input_type_selector == "clustering" | |
| 15 cluster | |
| 16 #if $input_type.mlst.mlst_checkbox | |
| 17 --mlst $input_type.mlst.mlst_path | |
| 18 #end if | |
| 19 #if $input_type.snp.snp_checkbox | |
| 20 --snp $input_type.snp.snp_path | |
| 21 #end if | |
| 22 #if $input_type.cnv.cnv_checkbox | |
| 23 --cnv $input_type.cnv.cnv_path | |
| 24 #end if | |
| 25 #if $input_type.spoligo.spoligo_checkbox | |
| 26 --spoligo $input_type.spoligo.spoligo_path | |
| 27 #end if | |
| 28 #end if | |
| 10 ]]></command> | 29 ]]></command> |
| 11 | 30 |
| 31 | |
| 12 <inputs> | 32 <inputs> |
| 13 <param name="paths" type="data" label="Collection of calls" help="" optional="False" multiple="True"/> | 33 <conditional name="input_type"> |
| 34 <param name="input_type_selector" type="select" label="Concatenation of variant calls, or clustering files"> | |
| 35 <option value="variant">Variant Call Files</option> | |
| 36 <option value="clustering">Clustering/Distance Matrix Files</option> | |
| 37 </param> | |
| 38 <when value="variant"> | |
| 39 <param name="paths" type="data" label="Collection of calls" help="" optional="False" multiple="True"/> | |
| 40 </when> | |
| 41 <when value="clustering"> | |
| 42 <conditional name="mlst"> | |
| 43 <param name="mlst_checkbox" type="boolean" label="Include MLST"/> | |
| 44 <when value="true"> | |
| 45 <param name="mlst_path" type="data" label="MLST Clustering/Distance Matrix file" | |
| 46 format="txt,tabular"/> | |
| 47 </when> | |
| 48 </conditional> | |
| 49 <conditional name="snp"> | |
| 50 <param name="snp_checkbox" type="boolean" label="Include SNP"/> | |
| 51 <when value="true"> | |
| 52 <param name="snp_path" type="data" label="SNP Clustering/Distance Matrix file" | |
| 53 format="txt,tabular"/> | |
| 54 </when> | |
| 55 </conditional> | |
| 56 <conditional name="cnv"> | |
| 57 <param name="cnv_checkbox" type="boolean" label="Include CNV"/> | |
| 58 <when value="true"> | |
| 59 <param name="cnv_path" type="data" label="CNV Clustering/Distance Matrix file" | |
| 60 format="txt,tabular"/> | |
| 61 </when> | |
| 62 </conditional> | |
| 63 <conditional name="spoligo"> | |
| 64 <param name="spoligo_checkbox" type="boolean" label="Include Spoligotyping"/> | |
| 65 <when value="true"> | |
| 66 <param name="spoligo_path" type="data" label="Spoligotyping Clustering/Distance Matrix file" | |
| 67 format="txt,tabular"/> | |
| 68 </when> | |
| 69 </conditional> | |
| 70 </when> | |
| 71 </conditional> | |
| 14 </inputs> | 72 </inputs> |
| 15 | 73 |
| 16 <outputs> | 74 <outputs> |
| 17 <data name="output" label="Paths of ${on_string}" format="txt" from_work_dir="paths.txt"/> | 75 <data name="output" label="Paths of ${on_string}" format="txt" from_work_dir="paths.txt"/> |
| 18 </outputs> | 76 </outputs> |