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comparison genetrack.xml @ 6:fa85ca6c9cf8 draft

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author greg
date Sat, 21 Nov 2015 08:57:37 -0500
parents fd4daf02a338
children 497e3274f70b
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5:551630d1fae3 6:fa85ca6c9cf8
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
8 <command> 8 <command>
9 python $__tool_directory__/genetrack.py 9 python $__tool_directory__/genetrack.py
10 --input_format $input_format_cond.input_format 10 --input_format $input_format_cond.input_format
11 #if str($input_format_cond.input_format) == "ssccidx": 11 #if str($input_format_cond.input_format) == "scidx":
12 #for $i in $input_format_cond.input_ssccidx: 12 #for $i in $input_format_cond.input_scidx:
13 --input "${i}" "${i.hid}" 13 --input "${i}" "${i.hid}"
14 #end for 14 #end for
15 #elif str($input_format_cond.input_format) == "gff": 15 #elif str($input_format_cond.input_format) == "gff":
16 #for $i in $input_format_cond.input_gff: 16 #for $i in $input_format_cond.input_gff:
17 --input "${i}" "${i.hid}" 17 --input "${i}" "${i.hid}"
25 --chunk_size $chunk_size 25 --chunk_size $chunk_size
26 </command> 26 </command>
27 <inputs> 27 <inputs>
28 <conditional name="input_format_cond"> 28 <conditional name="input_format_cond">
29 <param name="input_format" type="select" label="Format of files for conversion"> 29 <param name="input_format" type="select" label="Format of files for conversion">
30 <option value="ssccidx">SsccIdx</option> 30 <option value="scidx" selected="True">ScIdx</option>
31 <option value="gff" selected="True">Gff</option> 31 <option value="gff">Gff</option>
32 </param> 32 </param>
33 <when value="ssccidx"> 33 <when value="scidx">
34 <param name="input_ssccidx" type="data" format="ssccidx" multiple="True" label="Predict peaks on" /> 34 <param name="input_scidx" type="data" format="scidx" multiple="True" label="Predict peaks on" />
35 </when> 35 </when>
36 <when value="gff"> 36 <when value="gff">
37 <param name="input_gff" type="data" format="gff" multiple="True" label="Predict peaks on" /> 37 <param name="input_gff" type="data" format="gff" multiple="True" label="Predict peaks on" />
38 </when> 38 </when>
39 </conditional> 39 </conditional>
62 <output_collection name="genetrack_output" type="list"> 62 <output_collection name="genetrack_output" type="list">
63 <element name="s5e20u10d10F3_on_data_1" file="genetrack_output2.gff" ftype="gff" /> 63 <element name="s5e20u10d10F3_on_data_1" file="genetrack_output2.gff" ftype="gff" />
64 </output_collection> 64 </output_collection>
65 </test> 65 </test>
66 <test> 66 <test>
67 <param name="input_ssccidx" value="genetrack_input3.ssccidx" ftype="ssccidx" /> 67 <param name="input_scidx" value="genetrack_input3.scidx" ftype="scidx" />
68 <param name="input_format" value="ssccidx" /> 68 <param name="input_format" value="scidx" />
69 <param name="sigma" value="5" /> 69 <param name="sigma" value="5" />
70 <param name="exclusion" value="20" /> 70 <param name="exclusion" value="20" />
71 <param name="up_width" value="10" /> 71 <param name="up_width" value="10" />
72 <param name="down_width" value="10" /> 72 <param name="down_width" value="10" />
73 <param name="filter" value="3" /> 73 <param name="filter" value="3" />
96 Genetrack takes a standard set of data on both the sense and antisense strands and smooths their relative reads. 96 Genetrack takes a standard set of data on both the sense and antisense strands and smooths their relative reads.
97 It then calls the peaks present in the smoothed dataset and uses those peak locations to calculate the final 97 It then calls the peaks present in the smoothed dataset and uses those peak locations to calculate the final
98 reads from surrounding reads. Finally, it ensures each peak is above a threshold and that two peaks are not 98 reads from surrounding reads. Finally, it ensures each peak is above a threshold and that two peaks are not
99 too close to each other. 99 too close to each other.
100 100
101 -----
102
101 **Options** 103 **Options**
102 104
103 * **Sigma to use when smoothing reads** - Sigma to use when smoothing reads to call peaks. 105 * **Sigma to use when smoothing reads** - Sigma to use when smoothing reads to call peaks.
104 * **Peak exclusion zone** - Exclusion zone around each peak that prevents others from being called. 106 * **Peak exclusion zone** - Exclusion zone around each peak that prevents others from being called.
105 * **Upstream width of called peaks** - Upstream width of called peaks. 107 * **Upstream width of called peaks** - Upstream width of called peaks.