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comparison rgToolFactory.xml @ 30:fb3fa6a2874d draft

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Citations added (thanks John!) and a few more output formats for Alistair Chilcott
author fubar
date Thu, 28 Aug 2014 02:22:39 -0400
parents 63082502722a
children 4162896b29bd
comparison
equal deleted inserted replaced
29:bff4c9bfabc7 30:fb3fa6a2874d
1 <tool id="rgTF" name="Tool Factory" version="1.11"> 1 <tool id="rgTF" name="Tool Factory" version="1.11">
2 <description>Makes scripts into tools</description> 2 <description>Run a script; make a tool!</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="1.3.18">graphicsmagick</requirement>
6 </requirements> 6 </requirements>
7 <command interpreter="python"> 7 <command interpreter="python">
18 --tool_desc "$makeMode.tool_desc" 18 --tool_desc "$makeMode.tool_desc"
19 --tool_version "$makeMode.tool_version" 19 --tool_version "$makeMode.tool_version"
20 --new_tool "$new_tool" 20 --new_tool "$new_tool"
21 --help_text "$helpme" 21 --help_text "$helpme"
22 #if $make_HTML.value=="yes": 22 #if $make_HTML.value=="yes":
23 --include_dependencies "${makeMode.include_deps}" 23 #if makeMode.include.deps.value=="yes":
24 --include_dependencies "yes"
25 #end if
24 #end if 26 #end if
27 --citations "$citeme"
25 #end if 28 #end if
26 #if $make_HTML.value=="yes": 29 #if $make_HTML.value=="yes":
27 --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes" 30 --output_dir "$html_file.files_path" --output_html "$html_file" --make_HTML "yes"
28 #else: 31 #else:
29 --output_dir "." 32 --output_dir "."
64 <param name="include_deps" type="select" label="Include ghostscript and graphicsmagick dependencies in generated tool" size="60" 67 <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"> 68 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> 69 <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> 70 <option value="yes" selected="true">Include dependencies so target installations will always work if HTML is being generated</option>
68 </param> 71 </param>
69 72 <repeat name="citations" title="Citation">
73 <conditional name="citation_type">
74 <param name="type" type="select" label="Citation Type">
75 <option value="doi">DOI</option>
76 <option value="bibtex">BibTeX</option>
77 </param>
78 <when value="doi">
79 <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." />
81 </when>
82 <when value="bibtex">
83 <param name="bibtex" label="BibTex" type="text" area="true"
84 size="8x120" help="Supply a BibTex entry that should be cited when this tool is used in published research." value="" >
85 <sanitizer>
86 <valid initial="string.printable">
87 </valid>
88 <mapping initial="none"/>
89 </sanitizer>
90 </param>
91 </when>
92 </conditional>
93 </repeat>
70 </when> 94 </when>
71 <when value = ""> 95 <when value = "">
72 </when> 96 </when>
73 </conditional> 97 </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" 98 <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"
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"> 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">
85 <option value="tabular" selected="true">Tabular</option> 109 <option value="tabular" selected="true">Tabular</option>
86 <option value="interval">Interval</option> 110 <option value="interval">Interval</option>
87 <option value="gz">gz</option> 111 <option value="gz">gz</option>
88 <option value="text">text</option> 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>
89 </param> 118 </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"> 119 <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> 120 <option value="Rscript" selected="true">Rscript</option>
92 <option value="python">python</option> 121 <option value="python">python</option>
93 <option value="perl">perl</option> 122 <option value="perl">perl</option>
123 <option value="bash">bash</option>
94 <option value="sh">sh</option> 124 <option value="sh">sh</option>
95 </param> 125 </param>
96 <param name="dynScript" label="Cut and paste the script to be executed here" type="text" value="" area="True" size="8x120" 126 <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')."> 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').">
98 <sanitizer> 128 <sanitizer>
107 <filter>make_TAB=="yes"</filter> 137 <filter>make_TAB=="yes"</filter>
108 <change_format> 138 <change_format>
109 <when input="out_format" value="interval" format="interval" /> 139 <when input="out_format" value="interval" format="interval" />
110 <when input="out_format" value="gz" format="gz" /> 140 <when input="out_format" value="gz" format="gz" />
111 <when input="out_format" value="text" format="text" /> 141 <when input="out_format" value="text" format="text" />
142 <when input="out_format" value="sam" format="sam" />
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" />
112 </change_format> 146 </change_format>
113 </data> 147 </data>
114 <data format="html" name="html_file" label="${tool_name}.html"> 148 <data format="html" name="html_file" label="${tool_name}.html">
115 <filter>make_HTML == "yes"</filter> 149 <filter>make_HTML == "yes"</filter>
116 </data> 150 </data>
121 <configfiles> 155 <configfiles>
122 <configfile name="runme">$dynScript</configfile> 156 <configfile name="runme">$dynScript</configfile>
123 <configfile name="helpme"> 157 <configfile name="helpme">
124 #if $makeMode.make_Tool == "yes": 158 #if $makeMode.make_Tool == "yes":
125 ${makeMode.help_text} 159 ${makeMode.help_text}
160 #end if
161 </configfile>
162 <configfile name="citeme">
163 #if $makeMode.make_Tool == "yes":
164 #for $citation in $makeMode.citations:
165 #if $citation.citation_type.type == "bibtex":
166 **ENTRY**bibtex
167 ${citation.citation_type.bibtex}
168 #else
169 **ENTRY**doi
170 ${citation.citation_type.doi}
171 #end if
172 #end for
126 #end if 173 #end if
127 </configfile> 174 </configfile>
128 </configfiles> 175 </configfiles>
129 <help> 176 <help>
130 177
308 .. _GTFI: https://bitbucket.org/fubar/galaxytoolfactory/issues 355 .. _GTFI: https://bitbucket.org/fubar/galaxytoolfactory/issues
309 .. _Paper: http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&amp;keytype=ref 356 .. _Paper: http://bioinformatics.oxfordjournals.org/cgi/reprint/bts573?ijkey=lczQh1sWrMwdYWJ&amp;keytype=ref
310 357
311 358
312 </help> 359 </help>
313 360 <citations>
361 <citation type="doi">10.1093/bioinformatics/bts573</citation>
362 </citations>
314 </tool> 363 </tool>
315 364
316 365