Mercurial > repos > fubar > toolfactory
comparison rgToolFactory.xml @ 41:8d28e32c71ff draft
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author | fubar |
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date | Fri, 29 Aug 2014 01:50:44 -0400 |
parents | 8603867451d8 |
children | 4b807bc775ad |
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40:8603867451d8 | 41:8d28e32c71ff |
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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> |