Mercurial > repos > greg > cwpair2
changeset 4:9ed566138ecb draft
Uploaded
| author | greg |
|---|---|
| date | Sat, 21 Nov 2015 09:01:46 -0500 |
| parents | 430a5bdc55a3 |
| children | 2e0ddcc726f9 |
| files | cwpair2.xml |
| diffstat | 1 files changed, 26 insertions(+), 114 deletions(-) [+] |
line wrap: on
line diff
--- a/cwpair2.xml Sat Nov 21 09:01:35 2015 -0500 +++ b/cwpair2.xml Sat Nov 21 09:01:46 2015 -0500 @@ -21,10 +21,7 @@ #elif str($threshold_format_cond.threshold_format) == "relative_threshold": --relative_threshold $threshold_format_cond.relative_threshold #end if - --output_files $output_files_cond.output_files - #if str($output_files_cond.output_files) == "all" - --plot_format $output_files_cond.plot_format - #end if + --output_files $output_files --sort_chromosome $sort_chromosome --sort_score $sort_score --statistics_output "$statistics_output" @@ -53,24 +50,12 @@ <param name="absolute_threshold" type="float" value="0.0" min="0.0" label="Absolute value to filter below" /> </when> </conditional> - <conditional name="output_files_cond"> - <param name="output_files" type="select" label="Restrict output to" help="Statistics will always be generated." > - <option value="simple" selected="True">matched pairs only (S)</option> - <option value="simple_orphan">matched pairs and orphans only (O,S)</option> - <option value="simple_orphan_detail">matched pairs, orphans and details only (D,O,S)</option> - <option value="all">no restrictions (output everything: C,D,F,O,P,S)</option> - </param> - <when value="simple" /> - <when value="simple_orphan" /> - <when value="simple_orphan_detail" /> - <when value="all"> - <param name="plot_format" type="select" label="Output format for graph"> - <option value="pdf" selected="True">Pdf</option> - <option value="png">Png</option> - <option value="svg">Svg</option> - </param> - </when> - </conditional> + <param name="output_files" type="select" label="Restrict output to" help="Statistics will always be generated." > + <option value="simple" selected="True">matched pairs only (S)</option> + <option value="simple_orphan">matched pairs and orphans only (O,S)</option> + <option value="simple_orphan_detail">matched pairs, orphans and details only (D,O,S)</option> + <option value="all">no restrictions (output everything: C,D,F,O,P,S)</option> + </param> <param name="sort_chromosome" type="select" label="Sort output by chromosomes in" help="Chromosome strings that are not numeric will not be sorted" > <option value="asc" selected="True">ascending order</option> <option value="desc">descending order</option> @@ -83,137 +68,65 @@ </inputs> <outputs> <collection name="closest_C_pdf" type="list" label="closest C: ${tool.name} on ${on_string}"> - <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "pdf" and method in ["all", "closest"]</filter> + <filter>output_files == "all" and method in ["all", "closest"]</filter> <discover_datasets pattern="(?P<designation>.*)" directory="closest_C" ext="pdf" visible="false" /> </collection> - <collection name="closest_C_png" type="list" label="closest C: ${tool.name} on ${on_string}"> - <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "png" and method in ["all", "closest"]</filter> - <discover_datasets pattern="(?P<designation>.*)" directory="closest_C" ext="png" visible="false" /> - </collection> - <collection name="closest_C_svg" type="list" label="closest C: ${tool.name} on ${on_string}"> - <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "svg" and method in ["all", "closest"]</filter> - <discover_datasets pattern="(?P<designation>.*)" directory="closest_C" ext="svg" visible="false" /> - </collection> <collection name="largest_C_pdf" type="list" label="largest C: ${tool.name} on ${on_string}"> - <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "pdf" and method in ["all", "largest"]</filter> + <filter>output_files == "all" and method in ["all", "largest"]</filter> <discover_datasets pattern="(?P<designation>.*)" directory="largest_C" ext="pdf" visible="false" /> </collection> - <collection name="largest_C_png" type="list" label="largest C: ${tool.name} on ${on_string}"> - <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "png" and method in ["all", "largest"]</filter> - <discover_datasets pattern="(?P<designation>.*)" directory="largest_C" ext="png" visible="false" /> - </collection> - <collection name="largest_C_svg" type="list" label="largest C: ${tool.name} on ${on_string}"> - <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "svg" and method in ["all", "largest"]</filter> - <discover_datasets pattern="(?P<designation>.*)" directory="largest_C" ext="svg" visible="false" /> - </collection> <collection name="mode_C_pdf" type="list" label="mode C: ${tool.name} on ${on_string}"> - <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "pdf" and method in ["all", "mode"]</filter> + <filter>output_files == "all" and method in ["all", "mode"]</filter> <discover_datasets pattern="(?P<designation>.*)" directory="mode_C" ext="pdf" visible="false" /> </collection> - <collection name="mode_C_png" type="list" label="mode C: ${tool.name} on ${on_string}"> - <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "png" and method in ["all", "mode"]</filter> - <discover_datasets pattern="(?P<designation>.*)" directory="mode_C" ext="png" visible="false" /> - </collection> - <collection name="mode_C_svg" type="list" label="mode C: ${tool.name} on ${on_string}"> - <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "svg" and method in ["all", "mode"]</filter> - <discover_datasets pattern="(?P<designation>.*)" directory="mode_C" ext="svg" visible="false" /> - </collection> <collection name="closest_D" type="list" label="closest D: ${tool.name} on ${on_string}"> - <filter>output_files_cond["output_files"] in ["all", "simple_orphan_detail"] and method in ["all", "closest"]</filter> + <filter>output_files in ["all", "simple_orphan_detail"] and method in ["all", "closest"]</filter> <discover_datasets pattern="(?P<designation>.*)" directory="closest_D" ext="tabular" visible="false" /> </collection> <collection name="largest_D" type="list" label="largest D: ${tool.name} on ${on_string}"> - <filter>output_files_cond["output_files"] in ["all", "simple_orphan_detail"] and method in ["all", "largest"]</filter> + <filter>output_files in ["all", "simple_orphan_detail"] and method in ["all", "largest"]</filter> <discover_datasets pattern="(?P<designation>.*)" directory="largest_D" ext="tabular" visible="false" /> </collection> <collection name="mode_D" type="list" label="mode D: ${tool.name} on ${on_string}"> - <filter>output_files_cond["output_files"] in ["all", "simple_orphan_detail"] and method in ["all", "mode"]</filter> + <filter>output_files in ["all", "simple_orphan_detail"] and method in ["all", "mode"]</filter> <discover_datasets pattern="(?P<designation>.*)" directory="mode_D" ext="tabular" visible="false" /> </collection> <collection name="closest_F_pdf" type="list" label="closest F: ${tool.name} on ${on_string}"> - <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "pdf" and method in ["all", "closest"]</filter> + <filter>output_files == "all" and method in ["all", "closest"]</filter> <discover_datasets pattern="(?P<designation>.*)" directory="closest_F" ext="pdf" visible="false" /> </collection> - <collection name="closest_F_png" type="list" label="closest F: ${tool.name} on ${on_string}"> - <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "png" and method in ["all", "closest"]</filter> - <discover_datasets pattern="(?P<designation>.*)" directory="closest_F" ext="png" visible="false" /> - </collection> - <collection name="closest_F_svg" type="list" label="closest F: ${tool.name} on ${on_string}"> - <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "svg" and method in ["all", "closest"]</filter> - <discover_datasets pattern="(?P<designation>.*)" directory="closest_F" ext="svg" visible="false" /> - </collection> <collection name="largest_F_pdf" type="list" label="largest F: ${tool.name} on ${on_string}"> - <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "pdf" and method in ["all", "largest"]</filter> + <filter>output_files == "all" and method in ["all", "largest"]</filter> <discover_datasets pattern="(?P<designation>.*)" directory="largest_F" ext="pdf" visible="false" /> </collection> - <collection name="largest_F_png" type="list" label="largest F: ${tool.name} on ${on_string}"> - <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "png" and method in ["all", "largest"]</filter> - <discover_datasets pattern="(?P<designation>.*)" directory="largest_F" ext="png" visible="false" /> - </collection> - <collection name="largest_F_svg" type="list" label="largest F: ${tool.name} on ${on_string}"> - <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "svg" and method in ["all", "largest"]</filter> - <discover_datasets pattern="(?P<designation>.*)" directory="largest_F" ext="svg" visible="false" /> - </collection> <collection name="mode_F_pdf" type="list" label="mode F: ${tool.name} on ${on_string}"> - <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "pdf" and method in ["all", "mode"]</filter> + <filter>output_files == "all" and method in ["all", "mode"]</filter> <discover_datasets pattern="(?P<designation>.*)" directory="mode_F" ext="pdf" visible="false" /> </collection> - <collection name="mode_F_png" type="list" label="mode F: ${tool.name} on ${on_string}"> - <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "png" and method in ["all", "mode"]</filter> - <discover_datasets pattern="(?P<designation>.*)" directory="mode_F" ext="png" visible="false" /> - </collection> - <collection name="mode_F_svg" type="list" label="mode F: ${tool.name} on ${on_string}"> - <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "svg" and method in ["all", "mode"]</filter> - <discover_datasets pattern="(?P<designation>.*)" directory="mode_F" ext="svg" visible="false" /> - </collection> <collection name="closest_O" type="list" label="closest O: ${tool.name} on ${on_string}"> - <filter>output_files_cond["output_files"] in ["all", "simple_orphan", "simple_orphan_detail"] and method in ["all", "closest"]</filter> + <filter>output_files in ["all", "simple_orphan", "simple_orphan_detail"] and method in ["all", "closest"]</filter> <discover_datasets pattern="(?P<designation>.*)" directory="closest_O" ext="tabular" visible="false" /> </collection> <collection name="largest_O" type="list" label="largest O: ${tool.name} on ${on_string}"> - <filter>output_files_cond["output_files"] in ["all", "simple_orphan", "simple_orphan_detail"] and method in ["all", "largest"]</filter> + <filter>output_files in ["all", "simple_orphan", "simple_orphan_detail"] and method in ["all", "largest"]</filter> <discover_datasets pattern="(?P<designation>.*)" directory="largest_O" ext="tabular" visible="false" /> </collection> <collection name="mode_O" type="list" label="mode O: ${tool.name} on ${on_string}"> - <filter>output_files_cond["output_files"] in ["all", "simple_orphan", "simple_orphan_detail"] and method in ["all", "mode"]</filter> + <filter>output_files in ["all", "simple_orphan", "simple_orphan_detail"] and method in ["all", "mode"]</filter> <discover_datasets pattern="(?P<designation>.*)" directory="mode_O" ext="tabular" visible="false" /> </collection> <collection name="closest_P_pdf" type="list" label="closest P: ${tool.name} on ${on_string}"> - <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "pdf" and method in ["all", "closest"]</filter> + <filter>output_files == "all" and method in ["all", "closest"]</filter> <discover_datasets pattern="(?P<designation>.*)" directory="closest_P" ext="pdf" visible="false" /> </collection> - <collection name="closest_P_png" type="list" label="closest P: ${tool.name} on ${on_string}"> - <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "png" and method in ["all", "closest"]</filter> - <discover_datasets pattern="(?P<designation>.*)" directory="closest_P" ext="png" visible="false" /> - </collection> - <collection name="closest_P_svg" type="list" label="closest P: ${tool.name} on ${on_string}"> - <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "svg" and method in ["all", "closest"]</filter> - <discover_datasets pattern="(?P<designation>.*)" directory="closest_P" ext="svg" visible="false" /> - </collection> <collection name="largest_P_pdf" type="list" label="largest P: ${tool.name} on ${on_string}"> - <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "pdf" and method in ["all", "largest"]</filter> + <filter>output_files == "all" and method in ["all", "largest"]</filter> <discover_datasets pattern="(?P<designation>.*)" directory="largest_P" ext="pdf" visible="false" /> </collection> - <collection name="largest_P_png" type="list" label="largest P: ${tool.name} on ${on_string}"> - <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "png" and method in ["all", "largest"]</filter> - <discover_datasets pattern="(?P<designation>.*)" directory="largest_P" ext="png" visible="false" /> - </collection> - <collection name="largest_P_svg" type="list" label="largest P: ${tool.name} on ${on_string}"> - <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "svg" and method in ["all", "largest"]</filter> - <discover_datasets pattern="(?P<designation>.*)" directory="largest_P" ext="svg" visible="false" /> - </collection> <collection name="mode_P_pdf" type="list" label="mode P: ${tool.name} on ${on_string}"> - <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "pdf" and method in ["all", "mode"]</filter> + <filter>output_files == "all" and method in ["all", "mode"]</filter> <discover_datasets pattern="(?P<designation>.*)" directory="mode_P" ext="pdf" visible="false" /> </collection> - <collection name="mode_P_png" type="list" label="mode P: ${tool.name} on ${on_string}"> - <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "png" and method in ["all", "mode"]</filter> - <discover_datasets pattern="(?P<designation>.*)" directory="mode_P" ext="png" visible="false" /> - </collection> - <collection name="mode_P_svg" type="list" label="mode P: ${tool.name} on ${on_string}"> - <filter>output_files_cond["output_files"] == "all" and output_files_cond['plot_format'] == "svg" and method in ["all", "mode"]</filter> - <discover_datasets pattern="(?P<designation>.*)" directory="mode_P" ext="svg" visible="false" /> - </collection> <collection name="closest_S" type="list" label="closest S: ${tool.name} on ${on_string}"> <filter>method in ["all", "closest"]</filter> <discover_datasets pattern="(?P<designation>.*)" directory="closest_S" ext="gff" visible="false" /> @@ -260,7 +173,6 @@ <param name="threshold_format" value="relative_threshold" /> <param name="relative_threshold" value="0.0" /> <param name="output_files" value="all" /> - <param name="plot_format" value="pdf" /> <param name="sort_chromosome" value="asc" /> <param name="sort_score" value="no" /> <output_collection name="closest_D" type="list"> @@ -316,13 +228,14 @@ or all (where the analysis is run for each method). A statistics dataset is generated and a collection of datasets is produced for each method as follows. -* **closest/largest/mode C** - the stastics graph in a specified format: pdf, png or svg +* **closest/largest/mode C** - the stastics graph in pdf format * **closest/largest/mode D** - the details in tabular format -* **closest/largest/mode F** - the final plots graph in a specified format: pdf, png or svg +* **closest/largest/mode F** - the final plots graph in pdf format * **closest/largest/mode O** - the orphans in tabular format -* **closest/largest/mode P** - the preview plots graph in a specified format: pdf, png or svg +* **closest/largest/mode P** - the preview plots graph in pdf format * **closest/largest/mode S** - the matched pairs in gff format +----- **Options** @@ -332,7 +245,6 @@ * **Distance downstream from a peak to allow a pair** - Distance downstream from a Watson peak to allow a Crick pair. * **Percentage of the 95 percentile value to filter below** - Percentage of the 95 percentile value below which to filter when using a relative threshold. * **Absolute value to filter below** - Absolute value below which to filter when using an absolute threshold. -* **Output format for graph** - Output format for graph. * **Sort output by chromosomes in** - Output will be sorted by chromsome in the specified order. * **Sort output by score?** - If yes, output will be sorted by score in the specified order. * **Summary output format** - Format for summary output.