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comparison rgToolFactory.xml @ 40:8603867451d8 draft

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Uploaded
author fubar
date Thu, 28 Aug 2014 06:18:31 -0400
parents 64f7bd086146
children 8d28e32c71ff
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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">