Mercurial > repos > fubar > toolfactory

comparison rgToolFactory.xml @ 41:8d28e32c71ff draft

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author fubar
date Fri, 29 Aug 2014 01:50:44 -0400
parents 8603867451d8
children 4b807bc775ad
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40:8603867451d8 41:8d28e32c71ff
10 #else: 10 #else:
11 rgToolFactory.py --script_path "$runme" --interpreter "$interpreter" 11 rgToolFactory.py --script_path "$runme" --interpreter "$interpreter"
12 --tool_name "$tool_name" --user_email "$__user_email__" 12 --tool_name "$tool_name" --user_email "$__user_email__"
13 #if $make_TAB.value=="yes": 13 #if $make_TAB.value=="yes":
14 --output_tab "$tab_file" 14 --output_tab "$tab_file"
15 --output_format "$output_format"
15 #end if 16 #end if
16 #if $makeMode.make_Tool=="yes": 17 #if $makeMode.make_Tool=="yes":
17 --make_Tool "$makeMode.make_Tool" 18 --make_Tool "$makeMode.make_Tool"
18 --tool_desc "$makeMode.tool_desc" 19 --tool_desc "$makeMode.tool_desc"
19 --tool_version "$makeMode.tool_version" 20 --tool_version "$makeMode.tool_version"
31 #else: 32 #else:
32 --output_dir "." 33 --output_dir "."
33 #end if 34 #end if
34 #if $input1 != 'None': 35 #if $input1 != 'None':
35 --input_tab "$input1" 36 --input_tab "$input1"
37 --input_formats "$input_formats"
36 #end if 38 #end if
37 #end if 39 #end if
38 </command> 40 </command>
39 <inputs> 41 <inputs>
40 <param name="input1" type="data" label="Select an input file from your history" optional="true" size="120" 42 <param name="input1" type="data" label="Select an input file from your history" optional="true" size="120"
41 help="Most scripts will need an input - your script MUST be ready for whatever format you choose"/> 43 help="Most scripts will need an input - your script MUST be ready for whatever format you choose"/>
44 <param name="input_formats" type="select" multiple="true" label="Select the datatype(s) that your tool/script accepts as input"
45 help="If your datatype is not listed here, it has to be added in galaxy's datatypes_conf.xml">
46 <options from_parameter="tool.app.datatypes_registry.upload_file_formats">
47 <column name="value" index="0"/>
48 </options>
49 </param>
42 <param name="tool_name" type="text" value="My dynamic script" label="New tool ID and title for outputs" size="60" 50 <param name="tool_name" type="text" value="My dynamic script" label="New tool ID and title for outputs" size="60"
43 help="This will become the toolshed repository name so please choose thoughtfully to avoid namespace clashes with other tool writers"> 51 help="This will become the toolshed repository name so please choose thoughtfully to avoid namespace clashes with other tool writers">
44 <sanitizer invalid_char=""> 52 <sanitizer invalid_char="">
45 <valid initial="string.letters,string.digits"/> 53 <valid initial="string.letters,string.digits"/>
46 </sanitizer> 54 </sanitizer>
78 <when value="doi"> 86 <when value="doi">
79 <param name="doi" label="DOI" type="text" value="" 87 <param name="doi" label="DOI" type="text" value=""
80 help="Supply a DOI (e.g. 10.1111/j.1740-9713.2007.00258.x) that should be cited when this tool is used in published research." /> 88 help="Supply a DOI (e.g. 10.1111/j.1740-9713.2007.00258.x) that should be cited when this tool is used in published research." />
81 </when> 89 </when>
82 <when value="bibtex"> 90 <when value="bibtex">
83 <param name="bibtex" label="BibTex" type="text" area="true" 91 <param name="bibtex" label="BibTex" type="text" area="true" size="8x120"
84 size="8x120" help="Supply a BibTex entry that should be cited when this tool is used in published research." value="" > 92 help="Supply a BibTex entry that should be cited when this tool is used in published research." value="" >
85 <sanitizer> 93 <sanitizer>
86 <valid initial="string.printable"> 94 <valid initial="string.printable">
87 </valid> 95 </valid>
88 <mapping initial="none"/> 96 <mapping initial="none"/>
89 </sanitizer> 97 </sanitizer>
103 <param name="make_TAB" type="select" label="Create a new (default tabular) history output with or without an HTML file specified above" 111 <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"> 112 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> 113 <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> 114 <option value="">I do not want a new history output file</option>
107 </param> 115 </param>
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"> 116 <param name="output_format" type="select" label="Select the datatype for the file your tool/script will write"
117 help="If your datatype is not listed here, it has to be added in galaxy's datatypes_conf.xml">
109 <options from_parameter="tool.app.datatypes_registry.upload_file_formats"> 118 <options from_parameter="tool.app.datatypes_registry.upload_file_formats">
110 <column name="value" index="0"/> 119 <column name="value" index="0"/>
111 </options> 120 </options>
112 </param> 121 </param>
113 <param name="interpreter" type="select" label="Select the interpreter for your code. This must be available on the path of the execution host"> 122 <param name="interpreter" type="select" label="Select the interpreter for your code. This must be available on the path of the execution host">
114 <option value="Rscript" selected="true">Rscript</option> 123 <option value="Rscript" selected="true">Rscript</option>
115 <option value="python">python</option> 124 <option value="python">python</option>
116 <option value="perl">perl</option> 125 <option value="perl">perl</option>
126 <option value="bash">bash</option>
117 <option value="sh">sh</option> 127 <option value="sh">sh</option>
118 </param> 128 </param>
119 <param name="dynScript" label="Cut and paste the script to be executed here" type="text" value="" area="True" size="8x120" 129 <param name="dynScript" label="Cut and paste the script to be executed here" type="text" value="" area="True" size="8x120"
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')."> 130 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').">
121 <sanitizer> 131 <sanitizer>
124 <mapping initial="none"/> 134 <mapping initial="none"/>
125 </sanitizer> 135 </sanitizer>
126 </param> 136 </param>
127 </inputs> 137 </inputs>
128 <outputs> 138 <outputs>
129 <data format="input" name="tab_file" label="${tool_name}.${out_format}"> 139 <data format="input" name="tab_file" label="${tool_name}.${output_format}">
130 <filter>make_TAB == "yes"</filter> 140 <filter>make_TAB == "yes"</filter>
131 <actions> 141 <actions>
132 <action type="format"> 142 <action type="format">
133 <option type="from_param" name="out_format" /> 143 <option type="from_param" name="output_format" />
134 </action> 144 </action>
135 </actions> 145 </actions>
136 </data> 146 </data>
137 <data format="html" name="html_file" label="${tool_name}.html"> 147 <data format="html" name="html_file" label="${tool_name}.html">
138 <filter>make_HTML == "yes"</filter> 148 <filter>make_HTML == "yes"</filter>