Mercurial > repos > greg > repmatch_gff3

comparison repmatch_gff3.xml @ 7:1807688a8a5f draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author greg
date Sat, 28 Nov 2015 14:54:42 -0500
parents 1cea96c461a2
children 29082971b47c
comparison
equal deleted inserted replaced
6:6df81aade62c 7:1807688a8a5f
20 --output_summary "$output_summary" 20 --output_summary "$output_summary"
21 #if str($output_files_cond.output_files) in ["all", "simple_orphan"]: 21 #if str($output_files_cond.output_files) in ["all", "simple_orphan"]:
22 --output_orphan "$output_orphan" 22 --output_orphan "$output_orphan"
23 #end if 23 #end if
24 #if str($output_files_cond.output_files) =="all": 24 #if str($output_files_cond.output_files) =="all":
25 --plot_format $output_files_cond.plot_format
26 --output_detail "$output_detail" 25 --output_detail "$output_detail"
27 --output_key "$output_key" 26 --output_key "$output_key"
28 --output_histogram "$output_histogram" 27 --output_histogram "$output_histogram"
29 #end if 28 #end if
30 </command> 29 </command>
46 <option value="simple">matched pairs only</option> 45 <option value="simple">matched pairs only</option>
47 <option value="simple_orphan">matched pairs and orphans only</option> 46 <option value="simple_orphan">matched pairs and orphans only</option>
48 </param> 47 </param>
49 <when value="simple" /> 48 <when value="simple" />
50 <when value="simple_orphan" /> 49 <when value="simple_orphan" />
51 <when value="all"> 50 <when value="all" />
52 <param name="plot_format" type="select" label="Output format for graph">
53 <option value="pdf" selected="True">Pdf</option>
54 <option value="png">Png</option>
55 <option value="svg">Svg</option>
56 </param>
57 </when>
58 </conditional> 51 </conditional>
59 </inputs> 52 </inputs>
60 <outputs> 53 <outputs>
61 <data name="output_summary" format="gff" label="Matched pairs: ${tool.name} on ${on_string}" /> 54 <data name="output_summary" format="gff" label="Matched pairs: ${tool.name} on ${on_string}" />
62 <data name="output_orphan" format="tabular" label="Orphans: ${tool.name} on ${on_string}"> 55 <data name="output_orphan" format="tabular" label="Orphans: ${tool.name} on ${on_string}">
68 <data name="output_key" format="tabular" label="Key: ${tool.name} on ${on_string}"> 61 <data name="output_key" format="tabular" label="Key: ${tool.name} on ${on_string}">
69 <filter>output_files_cond["output_files"] == "all"</filter> 62 <filter>output_files_cond["output_files"] == "all"</filter>
70 </data> 63 </data>
71 <data name="output_histogram" format="pdf" label="Histogram: ${tool.name} on ${on_string}"> 64 <data name="output_histogram" format="pdf" label="Histogram: ${tool.name} on ${on_string}">
72 <filter>output_files_cond["output_files"] == "all"</filter> 65 <filter>output_files_cond["output_files"] == "all"</filter>
73 <actions>
74 <action type="format">
75 <option type="from_param" name="output_files_cond.plot_format" />
76 </action>
77 </actions>
78 </data> 66 </data>
79 </outputs> 67 </outputs>
80 <tests> 68 <tests>
81 <param name="input" value="closest_s_input1.gff" ftype="gff" /> 69 <param name="input" value="closest_s_input1.gff" ftype="gff" />
82 <param name="input" value="largest_s_input1.gff" ftype="gff" /> 70 <param name="input" value="largest_s_input1.gff" ftype="gff" />
85 <param name="step" value="0" /> 73 <param name="step" value="0" />
86 <param name="replicates" value="2" /> 74 <param name="replicates" value="2" />
87 <param name="low_limit" value="-1000" /> 75 <param name="low_limit" value="-1000" />
88 <param name="up_limit" value="1000" /> 76 <param name="up_limit" value="1000" />
89 <param name="output_files" value="all" /> 77 <param name="output_files" value="all" />
90 <param name="plot_format" value="png" />
91 <output name="output_summary" file="summary_out1.gff" ftype="gff" /> 78 <output name="output_summary" file="summary_out1.gff" ftype="gff" />
92 <output name="output_orphan" file="orphan_out1.tabular" ftype="tabular" /> 79 <output name="output_orphan" file="orphan_out1.tabular" ftype="tabular" />
93 <output name="output_detail" file="orphan_detail1.tabular" ftype="tabular" /> 80 <output name="output_detail" file="orphan_detail1.tabular" ftype="tabular" />
94 <output name="output_key" file="key_out1.tabular" ftype="tabular" /> 81 <output name="output_key" file="key_out1.tabular" ftype="tabular" />
95 <output name="output_histogram" file="histogram_out1.pdf" ftype="pdf" compare="sim_size" /> 82 <output name="output_histogram" file="histogram_out1.pdf" ftype="pdf" compare="sim_size" />