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comparison rgToolFactory.xml @ 43:c5bfdb0f7041 draft

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author fubar
date Tue, 07 Oct 2014 18:50:49 -0400
parents 4b807bc775ad
children 417cba94d862
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42:4b807bc775ad 43:c5bfdb0f7041
1 <tool id="rgTF" name="Tool Factory" version="1.10"> 1 <tool id="rgTF" name="Tool Factory" version="1.11">
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="1.3.18">graphicsmagick</requirement> 5 <requirement type="package" version="1.3.20">graphicsmagick</requirement>
6 </requirements> 6 </requirements>
7 <command interpreter="python"> 7 <command interpreter="python">
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 $make_TAB.value=="yes":
14 --output_tab "$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 "$makeMode.tool_version"
20 --new_tool "$new_tool" 21 --new_tool "$new_tool"
21 --help_text "$helpme" 22 --help_text "$helpme"
22 #if $make_HTML.value=="yes": 23 #if $make_HTML.value=="yes":
23 --include_dependencies "${makeMode.include_deps}" 24 #if makeMode.include_deps.value=="yes":
25 --include_dependencies "yes"
26 #end if
24 #end if 27 #end if
28 --citations "$citeme"
25 #end if 29 #end if
26 #if $make_HTML.value=="yes": 30 #if $make_HTML.value=="yes":
27 --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes" 31 --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes"
28 #else: 32 #else:
29 --output_dir "." 33 --output_dir "."
30 #end if 34 #end if
31 #if $input1 != 'None': 35 #if $input1 != 'None':
32 --input_tab "$input1" 36 --input_tab "$input1"
37 --input_formats "$input_formats"
33 #end if 38 #end if
34 #end if 39 #end if
35 </command> 40 </command>
36 <inputs> 41 <inputs>
37 <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"
38 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>
39 <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"
40 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">
41 <sanitizer invalid_char=""> 52 <sanitizer invalid_char="">
42 <valid initial="string.letters,string.digits"/> 53 <valid initial="string.letters,string.digits"/>
43 </sanitizer> 54 </sanitizer>
64 <param name="include_deps" type="select" label="Include ghostscript and graphicsmagick dependencies in generated tool" size="60" 75 <param name="include_deps" type="select" label="Include ghostscript and graphicsmagick dependencies in generated tool" size="60"
65 help="If an HTML file is being created, including dependencies is recommended. Otherwise this setting has no effect"> 76 help="If an HTML file is being created, including dependencies is recommended. Otherwise this setting has no effect">
66 <option value="">Rely on system ghostscript and graphicsmagick rather than include these as dependencies</option> 77 <option value="">Rely on system ghostscript and graphicsmagick rather than include these as dependencies</option>
67 <option value="yes" selected="true">Include dependencies so target installations will always work if HTML is being generated</option> 78 <option value="yes" selected="true">Include dependencies so target installations will always work if HTML is being generated</option>
68 </param> 79 </param>
69 80 <repeat name="citations" title="Citation">
81 <conditional name="citation_type">
82 <param name="type" type="select" label="Citation Type">
83 <option value="doi">DOI</option>
84 <option value="bibtex">BibTeX</option>
85 </param>
86 <when value="doi">
87 <param name="doi" label="DOI" type="text" value=""
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." />
89 </when>
90 <when value="bibtex">
91 <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="" >
93 <sanitizer>
94 <valid initial="string.printable">
95 </valid>
96 <mapping initial="none"/>
97 </sanitizer>
98 </param>
99 </when>
100 </conditional>
101 </repeat>
70 </when> 102 </when>
71 <when value = ""> 103 <when value = "">
72 </when> 104 </when>
73 </conditional> 105 </conditional>
74 <param name="make_HTML" type="select" label="Create an HTML report with links to all output files and thumbnail links to PDF images" size="60" 106 <param name="make_HTML" type="select" label="Create an HTML report with links to all output files and thumbnail links to PDF images" size="60"
79 <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"
80 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">
81 <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>
82 <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>
83 </param> 115 </param>
84 <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"> 116 <param name="output_format" type="select" label="Select the datatype for the file your tool/script will write"
85 <option value="tabular" selected="true">Tabular</option> 117 help="If your datatype is not listed here, it has to be added in galaxy's datatypes_conf.xml">
86 <option value="interval">Interval</option> 118 <options from_parameter="tool.app.datatypes_registry.upload_file_formats">
87 <option value="gz">gz</option> 119 <column name="value" index="0"/>
88 <option value="text">text</option> 120 </options>
89 </param> 121 </param>
90 <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">
91 <option value="Rscript" selected="true">Rscript</option> 123 <option value="Rscript" selected="true">Rscript</option>
92 <option value="python">python</option> 124 <option value="python">python</option>
93 <option value="perl">perl</option> 125 <option value="perl">perl</option>
126 <option value="bash">bash</option>
94 <option value="sh">sh</option> 127 <option value="sh">sh</option>
95 </param> 128 </param>
96 <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"
97 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').">
98 <sanitizer> 131 <sanitizer>
101 <mapping initial="none"/> 134 <mapping initial="none"/>
102 </sanitizer> 135 </sanitizer>
103 </param> 136 </param>
104 </inputs> 137 </inputs>
105 <outputs> 138 <outputs>
106 <data format="tabular" name="tab_file" label="${tool_name}.${out_format}"> 139 <data format="input" name="tab_file" label="${tool_name}.${output_format}">
107 <filter>make_TAB=="yes"</filter> 140 <filter>make_TAB == "yes"</filter>
108 <change_format> 141 <actions>
109 <when input="out_format" value="interval" format="interval" /> 142 <action type="format">
110 <when input="out_format" value="gz" format="gz" /> 143 <option type="from_param" name="output_format" />
111 <when input="out_format" value="text" format="text" /> 144 </action>
112 </change_format> 145 </actions>
113 </data> 146 </data>
114 <data format="html" name="html_file" label="${tool_name}.html"> 147 <data format="html" name="html_file" label="${tool_name}.html">
115 <filter>make_HTML == "yes"</filter> 148 <filter>make_HTML == "yes"</filter>
116 </data> 149 </data>
117 <data format="toolshed.gz" name="new_tool" label="${tool_name}.toolshed.gz"> 150 <data format="toolshed.gz" name="new_tool" label="${tool_name}.toolshed.gz">
121 <configfiles> 154 <configfiles>
122 <configfile name="runme">$dynScript</configfile> 155 <configfile name="runme">$dynScript</configfile>
123 <configfile name="helpme"> 156 <configfile name="helpme">
124 #if $makeMode.make_Tool == "yes": 157 #if $makeMode.make_Tool == "yes":
125 ${makeMode.help_text} 158 ${makeMode.help_text}
159 #end if
160 </configfile>
161 <configfile name="citeme">
162 #if $makeMode.make_Tool == "yes":
163 #for $citation in $makeMode.citations:
164 #if $citation.citation_type.type == "bibtex":
165 **ENTRY**bibtex
166 ${citation.citation_type.bibtex}
167 #else
168 **ENTRY**doi
169 ${citation.citation_type.doi}
170 #end if
171 #end for
126 #end if 172 #end if
127 </configfile> 173 </configfile>
128 </configfiles> 174 </configfiles>
129 <help> 175 <help>
130 176
308 .. _GTFI: https://bitbucket.org/fubar/galaxytoolfactory/issues 354 .. _GTFI: https://bitbucket.org/fubar/galaxytoolfactory/issues
309 .. _Paper: http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&amp;keytype=ref 355 .. _Paper: http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&amp;keytype=ref
310 356
311 357
312 </help> 358 </help>
313 359 <citations>
360 <citation type="doi">10.1093/bioinformatics/bts573</citation>
361 </citations>
314 </tool> 362 </tool>
315 363
316 364