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comparison split_file_to_collection.xml @ 1:6400d2b0175f draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/split_file_to_collection commit c9554ac81af24fc22435750fa4ef8c5c6fc1dc25
author bgruening
date Mon, 18 Feb 2019 15:20:07 -0500
parents e9d56b4c3209
children 0cf37301f754
comparison
equal deleted inserted replaced
0:e9d56b4c3209 1:6400d2b0175f
63 #end if 63 #end if
64 #if $split_parms.select_ftype != "tabular": 64 #if $split_parms.select_ftype != "tabular":
65 --file_names '$split_parms.newfilenames' 65 --file_names '$split_parms.newfilenames'
66 --file_ext '$split_parms.select_ftype' 66 --file_ext '$split_parms.select_ftype'
67 #end if 67 #end if
68 > '$log'
69 ]]></command> 68 ]]></command>
70 <inputs> 69 <inputs>
71 <conditional name="split_parms"> 70 <conditional name="split_parms">
72 <param name="select_ftype" type="select" label="Select the file type to split"> 71 <param name="select_ftype" type="select" label="Select the file type to split">
73 <option value="mgf">MGF</option> 72 <option value="mgf">MGF</option>
98 </mapping> 97 </mapping>
99 </sanitizer> 98 </sanitizer>
100 </param> 99 </param>
101 <param name="sub_regex" type="text" label="Pattern to replace match with" value="\1"> 100 <param name="sub_regex" type="text" label="Pattern to replace match with" value="\1">
102 <sanitizer> 101 <sanitizer>
103 <valid> 102 <valid>
104 <add preset="string.printable"/> 103 <add preset="string.printable"/>
105 <remove value="&#92;" /> 104 <remove value="&#92;" />
106 <remove value="&apos;" /> 105 <remove value="&apos;" />
107 </valid> 106 </valid>
108 <mapping initial="none"> 107 <mapping initial="none">
109 <add source="&#92;" target="__backslash__" /> 108 <add source="&#92;" target="__backslash__" />
110 <add source="&apos;" target="__sq__"/> 109 <add source="&apos;" target="__sq__"/>
111 </mapping> 110 </mapping>
112 </sanitizer> 111 </sanitizer>
113 </param> 112 </param>
114 </when> 113 </when>
115 <when value="row"> 114 <when value="row">
116 <expand macro="numnew_fname"/> 115 <expand macro="numnew_fname"/>
146 </collection> 145 </collection>
147 <collection name="list_output_fastq" type="list" label="${tool.name} on ${on_string}: output collection"> 146 <collection name="list_output_fastq" type="list" label="${tool.name} on ${on_string}: output collection">
148 <discover_datasets pattern="__name__" directory="out" visible="false" format="fastq"/> 147 <discover_datasets pattern="__name__" directory="out" visible="false" format="fastq"/>
149 <filter>split_parms['select_ftype'] == "fastq"</filter> 148 <filter>split_parms['select_ftype'] == "fastq"</filter>
150 </collection> 149 </collection>
151 <data name="log" format="txt" label="${tool.name} on ${on_string}: log" />
152 </outputs> 150 </outputs>
153 <tests> 151 <tests>
154 <test> 152 <test>
155 <param name="input" value="test.tabular" ftype="tabular"/> 153 <param name="input" value="test.tabular" ftype="tabular"/>
156 <param name="select_ftype" value="tabular"/> 154 <param name="select_ftype" value="tabular"/>
278 <citations> 276 <citations>
279 <citation type="bibtex"> 277 <citation type="bibtex">
280 @misc{githubsplit, 278 @misc{githubsplit,
281 author = {Easterly, Caleb}, 279 author = {Easterly, Caleb},
282 year = {2018}, 280 year = {2018},
283 title = {split_file_to_collection: a Galaxy tool}, 281 title = {A Galxy tool for splitting a file into a collection},
284 publisher = {GitHub}, 282 publisher = {GitHub},
285 journal = {GitHub repository}, 283 journal = {GitHub repository},
286 url = {https://github.com/galaxyproteomics/tools-galaxyp/tools/split_file_to_collection}, 284 url = {https://github.com/bgruening/galaxytools/tools/text_processing/split_file_to_collection},
287 }</citation> 285 }</citation>
288 </citations> 286 </citations>
289 </tool> 287 </tool>