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comparison rgToolFactory.xml @ 44:417cba94d862 draft

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Uploaded
author fubar
date Tue, 07 Oct 2014 20:23:23 -0400
parents c5bfdb0f7041
children 7b34711416d2
comparison
equal deleted inserted replaced
43:c5bfdb0f7041 44:417cba94d862
1 <tool id="rgTF" name="Tool Factory" version="1.11"> 1 <tool id="rgTF" name="Tool Factory" version="1.12">
2 <description>Makes scripts into tools</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>
8 #if ( $__user_email__ not in $__admin_users__ ): 8 #if ( $__user_email__ not in $__admin_users__ ):
9 rgToolFactory.py --bad_user $__user_email__ 9 rgToolFactory.py --bad_user $__user_email__
10 #else: 10 #else:
11 rgToolFactory.py --script_path "$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 $make_TAB=="yes":
14 --output_tab "$tab_file" 14 --output_tab "$tab_file"
15 --output_format "$output_format" 15 --output_format "$output_format"
16 #end if 16 #end if
17 #if $makeMode.make_Tool=="yes": 17 #if $makeMode.make_Tool == "yes":
18 --make_Tool "$makeMode.make_Tool" 18 --make_Tool "yes"
19 --tool_desc "$makeMode.tool_desc" 19 --tool_desc "$makeMode.tool_desc"
20 --tool_version "$makeMode.tool_version" 20 --tool_version "$makeMode.tool_version"
21 --new_tool "$new_tool" 21 --new_tool "$new_tool"
22 --help_text "$helpme" 22 --help_text "$helpme"
23 #if $make_HTML.value=="yes":
24 #if makeMode.include_deps.value=="yes":
25 --include_dependencies "yes"
26 #end if
27 #end if
28 --citations "$citeme" 23 --citations "$citeme"
29 #end if 24 --include_dependencies "yes"
30 #if $make_HTML.value=="yes": 25 #end if
31 --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes" 26
27 #if $make_HTML=="yes":
28 --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes"
32 #else: 29 #else:
33 --output_dir "." 30 --output_dir "."
34 #end if 31 #end if
35 #if $input1 != 'None': 32 #if $input1 != 'None':
36 --input_tab "$input1" 33 --input_tab "$input1"
65 help="Supply a brief tool description for the Galaxy tool menu entry (optional - appears after the tool name)" /> 62 help="Supply a brief tool description for the Galaxy tool menu entry (optional - appears after the tool name)" />
66 <param name="help_text" label="Tool form documentation and help text for users" type="text" area="true" 63 <param name="help_text" label="Tool form documentation and help text for users" type="text" area="true"
67 size="8x120" value="**What it Does**" 64 size="8x120" value="**What it Does**"
68 help="Supply the brief user documentation to appear on the new tool form as reStructured text - http://docutils.sourceforge.net/docs/ref/rst/restructuredtext.html" > 65 help="Supply the brief user documentation to appear on the new tool form as reStructured text - http://docutils.sourceforge.net/docs/ref/rst/restructuredtext.html" >
69 <sanitizer> 66 <sanitizer>
70 <valid initial="string.printable"> 67 <valid initial="string.printable"/>
71 </valid>
72 <mapping initial="none"/> 68 <mapping initial="none"/>
73 </sanitizer> 69 </sanitizer>
74 </param> 70 </param>
75 <param name="include_deps" type="select" label="Include ghostscript and graphicsmagick dependencies in generated tool" size="60" 71 <param name="include_deps" type="select" label="Include ghostscript and graphicsmagick dependencies in generated tool" size="60"
76 help="If an HTML file is being created, including dependencies is recommended. Otherwise this setting has no effect"> 72 help="If an HTML file is being created, including dependencies is recommended. Otherwise this setting has no effect">
89 </when> 85 </when>
90 <when value="bibtex"> 86 <when value="bibtex">
91 <param name="bibtex" label="BibTex" type="text" area="true" size="8x120" 87 <param name="bibtex" label="BibTex" type="text" area="true" size="8x120"
92 help="Supply a BibTex entry that should be cited when this tool is used in published research." value="" > 88 help="Supply a BibTex entry that should be cited when this tool is used in published research." value="" >
93 <sanitizer> 89 <sanitizer>
94 <valid initial="string.printable"> 90 <valid initial="string.printable"/>
95 </valid>
96 <mapping initial="none"/> 91 <mapping initial="none"/>
97 </sanitizer> 92 </sanitizer>
98 </param> 93 </param>
99 </when> 94 </when>
100 </conditional> 95 </conditional>
153 </outputs> 148 </outputs>
154 <configfiles> 149 <configfiles>
155 <configfile name="runme">$dynScript</configfile> 150 <configfile name="runme">$dynScript</configfile>
156 <configfile name="helpme"> 151 <configfile name="helpme">
157 #if $makeMode.make_Tool == "yes": 152 #if $makeMode.make_Tool == "yes":
158 ${makeMode.help_text} 153 $makeMode.help_text
159 #end if 154 #end if
160 </configfile> 155 </configfile>
161 <configfile name="citeme"> 156 <configfile name="citeme">
162 #if $makeMode.make_Tool == "yes": 157 #if $makeMode.make_Tool == "yes":
163 #for $citation in $makeMode.citations: 158 #for $citation in $makeMode.citations:
164 #if $citation.citation_type.type == "bibtex": 159 #if $citation.citation_type.type == "bibtex":
165 **ENTRY**bibtex 160 **ENTRY**bibtex
166 ${citation.citation_type.bibtex} 161 ${citation.citation_type.bibtex}
167 #else 162 #else:
168 **ENTRY**doi 163 **ENTRY**doi
169 ${citation.citation_type.doi} 164 ${citation.citation_type.doi}
170 #end if 165 #end if
171 #end for 166 #end for
172 #end if 167 #end if
173 </configfile> 168 </configfile>
174 </configfiles> 169 </configfiles>
175 <help> 170 <help>
176 171