Mercurial > repos > fubar > toolfactory
comparison rgToolFactory.xml @ 40:8603867451d8 draft
Uploaded
| author | fubar |
|---|---|
| date | Thu, 28 Aug 2014 06:18:31 -0400 |
| parents | 64f7bd086146 |
| children | 8d28e32c71ff |
comparison
equal
deleted
inserted
replaced
| 39:64f7bd086146 | 40:8603867451d8 |
|---|---|
| 1 <tool id="rgTF" name="Tool Factory" version="1.12"> | 1 <tool id="rgTF" name="Tool Factory" version="1.11"> |
| 2 <description>Run a script; make a tool!</description> | 2 <description>Makes scripts into tools</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="package" version="9.10">ghostscript</requirement> | 4 <requirement type="package" version="9.10">ghostscript</requirement> |
| 5 <requirement type="package" version="1.3.20">graphicsmagick</requirement> | 5 <requirement type="package" version="1.3.20">graphicsmagick</requirement> |
| 6 </requirements> | 6 </requirements> |
| 7 <command interpreter="python"> | 7 <command interpreter="python"> |
| 103 <param name="make_TAB" type="select" label="Create a new (default tabular) history output with or without an HTML file specified above" | 103 <param name="make_TAB" type="select" label="Create a new (default tabular) history output with or without an HTML file specified above" |
| 104 help="This is useful if your script creates a single new tabular file you want to appear in the history after the tool executes"> | 104 help="This is useful if your script creates a single new tabular file you want to appear in the history after the tool executes"> |
| 105 <option value="yes" selected="true">My script writes to a new history output</option> | 105 <option value="yes" selected="true">My script writes to a new history output</option> |
| 106 <option value="">I do not want a new history output file</option> | 106 <option value="">I do not want a new history output file</option> |
| 107 </param> | 107 </param> |
| 108 <param name="out_format" type="select" label="Galaxy datatype for your tool's output file if any" help="You may need to edit the xml to extend this list"> | 108 <param name="out_format" type="select" label="Select the datatype that your tool/script produces" help="If your datatype is not listed here, it has to be added in galaxy's datatypes_conf.xml"> |
| 109 <option value="tabular" selected="true">Tabular</option> | 109 <options from_parameter="tool.app.datatypes_registry.upload_file_formats"> |
| 110 <option value="interval">Interval</option> | 110 <column name="value" index="0"/> |
| 111 <option value="gz">gz</option> | 111 </options> |
| 112 <option value="text">text</option> | |
| 113 <option value="sam">sam</option> | |
| 114 <option value="bam">bam</option> | |
| 115 <option value="fastqsanger">fastqsanger</option> | |
| 116 <option value="fastq">fastq</option> | |
| 117 <option value="fasta">fasta</option> | |
| 118 </param> | 112 </param> |
| 119 <param name="interpreter" type="select" label="Select the interpreter for your code. This must be available on the path of the execution host"> | 113 <param name="interpreter" type="select" label="Select the interpreter for your code. This must be available on the path of the execution host"> |
| 120 <option value="Rscript" selected="true">Rscript</option> | 114 <option value="Rscript" selected="true">Rscript</option> |
| 121 <option value="python">python</option> | 115 <option value="python">python</option> |
| 122 <option value="perl">perl</option> | 116 <option value="perl">perl</option> |
| 123 <option value="bash">bash</option> | |
| 124 <option value="sh">sh</option> | 117 <option value="sh">sh</option> |
| 125 </param> | 118 </param> |
| 126 <param name="dynScript" label="Cut and paste the script to be executed here" type="text" value="" area="True" size="8x120" | 119 <param name="dynScript" label="Cut and paste the script to be executed here" type="text" value="" area="True" size="8x120" |
| 127 help="Script must deal with two command line parameters: Path to input tabular file path (or 'None' if none selected) and path to output tabular history file (or 'None')."> | 120 help="Script must deal with two command line parameters: Path to input tabular file path (or 'None' if none selected) and path to output tabular history file (or 'None')."> |
| 128 <sanitizer> | 121 <sanitizer> |
| 131 <mapping initial="none"/> | 124 <mapping initial="none"/> |
| 132 </sanitizer> | 125 </sanitizer> |
| 133 </param> | 126 </param> |
| 134 </inputs> | 127 </inputs> |
| 135 <outputs> | 128 <outputs> |
| 136 <data format="tabular" name="tab_file" label="${tool_name}.${out_format}"> | 129 <data format="input" name="tab_file" label="${tool_name}.${out_format}"> |
| 137 <filter>make_TAB=="yes"</filter> | 130 <filter>make_TAB == "yes"</filter> |
| 138 <change_format> | 131 <actions> |
| 139 <when input="out_format" value="interval" format="interval" /> | 132 <action type="format"> |
| 140 <when input="out_format" value="gz" format="gz" /> | 133 <option type="from_param" name="out_format" /> |
| 141 <when input="out_format" value="text" format="text" /> | 134 </action> |
| 142 <when input="out_format" value="sam" format="sam" /> | 135 </actions> |
| 143 <when input="out_format" value="bam" format="bam" /> | |
| 144 <when input="out_format" value="fastqsanger" format="fastqsanger" /> | |
| 145 <when input="out_format" value="fastq" format="fastq" /> | |
| 146 </change_format> | |
| 147 </data> | 136 </data> |
| 148 <data format="html" name="html_file" label="${tool_name}.html"> | 137 <data format="html" name="html_file" label="${tool_name}.html"> |
| 149 <filter>make_HTML == "yes"</filter> | 138 <filter>make_HTML == "yes"</filter> |
| 150 </data> | 139 </data> |
| 151 <data format="toolshed.gz" name="new_tool" label="${tool_name}.toolshed.gz"> | 140 <data format="toolshed.gz" name="new_tool" label="${tool_name}.toolshed.gz"> |