Mercurial > repos > dave > transit_resampling

annotate transit_resampling.xml @ 0:c641d7e020bf draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit commit bb1afe7092cd4f9440d3434379a93270907bf175
author dave
date Mon, 05 Nov 2018 14:26:52 -0500
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
c641d7e020bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit commit bb1afe7092cd4f9440d3434379a93270907bf175
dave
parents:
diff changeset
1 <?xml version="1.0"?>
c641d7e020bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit commit bb1afe7092cd4f9440d3434379a93270907bf175
dave
parents:
diff changeset
2 <tool id="transit_resampling" name="Resampling:" version="@VERSION@+galaxy0">
c641d7e020bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit commit bb1afe7092cd4f9440d3434379a93270907bf175
dave
parents:
diff changeset
3 <description>determine per-gene p-values</description>
c641d7e020bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit commit bb1afe7092cd4f9440d3434379a93270907bf175
dave
parents:
diff changeset
4 <macros>
c641d7e020bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit commit bb1afe7092cd4f9440d3434379a93270907bf175
dave
parents:
diff changeset
5 <import>macros.xml</import>
c641d7e020bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit commit bb1afe7092cd4f9440d3434379a93270907bf175
dave
parents:
diff changeset
6 </macros>
c641d7e020bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit commit bb1afe7092cd4f9440d3434379a93270907bf175
dave
parents:
diff changeset
7 <expand macro="requirements" />
c641d7e020bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit commit bb1afe7092cd4f9440d3434379a93270907bf175
dave
parents:
diff changeset
8 <command detect_errors="exit_code"><![CDATA[
c641d7e020bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit commit bb1afe7092cd4f9440d3434379a93270907bf175
dave
parents:
diff changeset
9 @LINK_INPUTS@
c641d7e020bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit commit bb1afe7092cd4f9440d3434379a93270907bf175
dave
parents:
diff changeset
10 #set $control_files = ','.join(['control_file_%d.wig' % idx for idx, _ in enumerate(str($controls).split(','))])
c641d7e020bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit commit bb1afe7092cd4f9440d3434379a93270907bf175
dave
parents:
diff changeset
11 #for idx, filename in enumerate(str($controls).split(',')):
c641d7e020bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit commit bb1afe7092cd4f9440d3434379a93270907bf175
dave
parents:
diff changeset
12 ln -s '$filename' control_file_${idx}.wig &&
c641d7e020bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit commit bb1afe7092cd4f9440d3434379a93270907bf175
dave
parents:
diff changeset
13 #end for
c641d7e020bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit commit bb1afe7092cd4f9440d3434379a93270907bf175
dave
parents:
diff changeset
14 transit resampling $input_files $control_files annotation.dat transit_out.txt
c641d7e020bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit commit bb1afe7092cd4f9440d3434379a93270907bf175
dave
parents:
diff changeset
15 @STANDARD_OPTIONS@
c641d7e020bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit commit bb1afe7092cd4f9440d3434379a93270907bf175
dave
parents:
diff changeset
16 -s $samples -n $normalization $histogram $adaptive $exclude_zero $pseudo $loess
c641d7e020bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit commit bb1afe7092cd4f9440d3434379a93270907bf175
dave
parents:
diff changeset
17 ]]>
c641d7e020bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit commit bb1afe7092cd4f9440d3434379a93270907bf175
dave
parents:
diff changeset
18 </command>
c641d7e020bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit commit bb1afe7092cd4f9440d3434379a93270907bf175
dave
parents:
diff changeset
19 <inputs>
c641d7e020bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit commit bb1afe7092cd4f9440d3434379a93270907bf175
dave
parents:
diff changeset
20 <expand macro="standard_inputs">
c641d7e020bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit commit bb1afe7092cd4f9440d3434379a93270907bf175
dave
parents:
diff changeset
21 <param name="controls" type="data" format="wig" multiple="true" label="Control .wig files" />
c641d7e020bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit commit bb1afe7092cd4f9440d3434379a93270907bf175
dave
parents:
diff changeset
22 <param name="samples" argument="-s" type="integer" value="10000" label="Number of samples" />
c641d7e020bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit commit bb1afe7092cd4f9440d3434379a93270907bf175
dave
parents:
diff changeset
23 <param name="normalization" argument="-n" type="select" label="Normalization method">
c641d7e020bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit commit bb1afe7092cd4f9440d3434379a93270907bf175
dave
parents:
diff changeset
24 <option value="TTR">TTR</option>
c641d7e020bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit commit bb1afe7092cd4f9440d3434379a93270907bf175
dave
parents:
diff changeset
25 </param>
c641d7e020bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit commit bb1afe7092cd4f9440d3434379a93270907bf175
dave
parents:
diff changeset
26 <param name="histogram" argument="-h" type="boolean" truevalue="-h" falsevalue="" label="Output histogram of the permutations" />
c641d7e020bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit commit bb1afe7092cd4f9440d3434379a93270907bf175
dave
parents:
diff changeset
27 <param name="adaptive" argument="-a" type="boolean" truevalue="-a" falsevalue="" label="Perform adaptive resampling" />
c641d7e020bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit commit bb1afe7092cd4f9440d3434379a93270907bf175
dave
parents:
diff changeset
28 <param name="exclude_zero" argument="-ez" type="boolean" truevalue="-ez" falsevalue="" label="Exclude rows with zero accross conditions" />
c641d7e020bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit commit bb1afe7092cd4f9440d3434379a93270907bf175
dave
parents:
diff changeset
29 <param name="pseudo" argument="-pc" type="boolean" truevalue="-pc" falsevalue="" label="Add pseudocounts at each site" />
c641d7e020bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit commit bb1afe7092cd4f9440d3434379a93270907bf175
dave
parents:
diff changeset
30 <param name="loess" argument="-l" type="boolean" truevalue="-l" falsevalue="" label="Perform LOESS Correction" help="Helps remove possible genomic position bias." />
c641d7e020bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit commit bb1afe7092cd4f9440d3434379a93270907bf175
dave
parents:
diff changeset
31
c641d7e020bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit commit bb1afe7092cd4f9440d3434379a93270907bf175
dave
parents:
diff changeset
32 </expand>
c641d7e020bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit commit bb1afe7092cd4f9440d3434379a93270907bf175
dave
parents:
diff changeset
33 </inputs>
c641d7e020bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit commit bb1afe7092cd4f9440d3434379a93270907bf175
dave
parents:
diff changeset
34 <outputs>
c641d7e020bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit commit bb1afe7092cd4f9440d3434379a93270907bf175
dave
parents:
diff changeset
35 <expand macro="outputs" />
c641d7e020bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit commit bb1afe7092cd4f9440d3434379a93270907bf175
dave
parents:
diff changeset
36 </outputs>
c641d7e020bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit commit bb1afe7092cd4f9440d3434379a93270907bf175
dave
parents:
diff changeset
37 <tests>
c641d7e020bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit commit bb1afe7092cd4f9440d3434379a93270907bf175
dave
parents:
diff changeset
38 <test>
c641d7e020bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit commit bb1afe7092cd4f9440d3434379a93270907bf175
dave
parents:
diff changeset
39 <param name="inputs" ftype="wig" value="transit-in1-rep1.wig,transit-in1-rep2.wig" />
c641d7e020bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit commit bb1afe7092cd4f9440d3434379a93270907bf175
dave
parents:
diff changeset
40 <param name="controls" ftype="wig" value="transit-co1-rep1.wig,transit-co1-rep2.wig,transit-co1-rep3.wig" />
c641d7e020bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit commit bb1afe7092cd4f9440d3434379a93270907bf175
dave
parents:
diff changeset
41 <param name="annotation" ftype="gff3" value="transit-in1.gff3" />
c641d7e020bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit commit bb1afe7092cd4f9440d3434379a93270907bf175
dave
parents:
diff changeset
42 <param name="samples" value="1000" />
c641d7e020bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit commit bb1afe7092cd4f9440d3434379a93270907bf175
dave
parents:
diff changeset
43 <param name="burnin" value="100" />
c641d7e020bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit commit bb1afe7092cd4f9440d3434379a93270907bf175
dave
parents:
diff changeset
44 <output name="sites" file="gumbel-sites1.txt" ftype="tabular" />
c641d7e020bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit commit bb1afe7092cd4f9440d3434379a93270907bf175
dave
parents:
diff changeset
45 <output name="genes" file="gumbel-genes1.txt" ftype="tabular" />
c641d7e020bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit commit bb1afe7092cd4f9440d3434379a93270907bf175
dave
parents:
diff changeset
46 </test>
c641d7e020bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit commit bb1afe7092cd4f9440d3434379a93270907bf175
dave
parents:
diff changeset
47 </tests>
c641d7e020bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit commit bb1afe7092cd4f9440d3434379a93270907bf175
dave
parents:
diff changeset
48 <help>
c641d7e020bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit commit bb1afe7092cd4f9440d3434379a93270907bf175
dave
parents:
diff changeset
49 <![CDATA[
c641d7e020bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit commit bb1afe7092cd4f9440d3434379a93270907bf175
dave
parents:
diff changeset
50 The re-sampling method is a comparative analysis the allows that can be used to determine conditional essentiality of genes. It is based on a permutation test, and is capable of determining read-counts that are significantly different across conditions.
c641d7e020bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit commit bb1afe7092cd4f9440d3434379a93270907bf175
dave
parents:
diff changeset
51 ]]></help>
c641d7e020bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit commit bb1afe7092cd4f9440d3434379a93270907bf175
dave
parents:
diff changeset
52 <expand macro="citations" />
c641d7e020bf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transit commit bb1afe7092cd4f9440d3434379a93270907bf175
dave
parents:
diff changeset
53 </tool>