Mercurial > repos > mvdbeek > damidseq_polii_gene_call

annotate damid_polII_gene_call.xml @ 1:83ca801f21f9 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/damidseq_polII_gene_call commit 98722d2ca8205595f032361072aaab450e5f4f83
author mvdbeek
date Fri, 04 Jan 2019 14:43:20 -0500
parents 1b5bd3b955ed
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
1b5bd3b955ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
1 <tool id="damidseq_polII_gene_call" name="Calculate polII occupancy" version="1.0.2">
1b5bd3b955ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
2 <description>from DamIDseq data</description>
1b5bd3b955ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
3 <requirements>
1
83ca801f21f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 98722d2ca8205595f032361072aaab450e5f4f83
mvdbeek
parents: 0
diff changeset
4 <requirement type="package" version="3.5">r-base</requirement>
0
1b5bd3b955ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
5 </requirements>
1b5bd3b955ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
6 <version_command><![CDATA[Rscript '$__tool_directory__/polii.gene.call' | grep -o "v.*"]]></version_command>
1b5bd3b955ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
7 <command detect_errors="aggressive"><![CDATA[
1b5bd3b955ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
8 ln -fs '$genes' genes.gff &&
1b5bd3b955ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
9 ln -fs '$input_file' input.$input_file.ext &&
1b5bd3b955ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
10 Rscript '$__tool_directory__/polii.gene.call' --genes.file=genes.gff input.$input_file.ext --iter=$iter --fdr=$fdr &&
1b5bd3b955ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
11 mv *.details.csv details.csv &&
1b5bd3b955ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
12 mv *.genes genes.csv
1b5bd3b955ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
13 ]]></command>
1b5bd3b955ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
14 <inputs>
1b5bd3b955ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
15 <param name="input_file" type="data" format="gff,bed,bedgraph" label="Select dam-fusion/dam ratio files" help="You can use damidseq_core to produce this file."/>
1b5bd3b955ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
16 <param name="genes" type="data" format="gff" label="Select a GFF file containing genes for which to calculate occupancy"/>
1b5bd3b955ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
17 <param name="iter" type="integer" min="1" value="50000" label="Number of iterations for calculation of FDR"/>
1b5bd3b955ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
18 <param name="fdr" type="float" min="0" max="1" value="0.01" label="FDR cutoff for gene list"/>
1b5bd3b955ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
19 </inputs>
1b5bd3b955ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
20 <outputs>
1b5bd3b955ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
21 <data name="details" format="csv" from_work_dir="details.csv" label="${tool.name} gene details on ${on_string}"/>
1b5bd3b955ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
22 <data name="sig_genes" format="csv" from_work_dir="genes.csv" label="${tool.name} genes on ${on_string}"/>
1b5bd3b955ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
23 </outputs>
1b5bd3b955ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
24 <tests>
1b5bd3b955ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
25 <test>
1b5bd3b955ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
26 <param name="input_file" value="polII.bed" ftype="bedgraph"/>
1b5bd3b955ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
27 <param name="genes" value="genes.gff" ftype="gff"/>
1b5bd3b955ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
28 <param name="fdr" value="1"/>
1b5bd3b955ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
29 <param name="iter" value="500"/>
1b5bd3b955ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
30 <output name="details" value="details.csv" compare="sim_size"/>
1b5bd3b955ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
31 <output name="sig_genes" value="genes.csv" compare="sim_size"/>
1b5bd3b955ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
32 </test>
1b5bd3b955ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
33 </tests>
1b5bd3b955ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
34 <help><![CDATA[
1b5bd3b955ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
35 What it does
1b5bd3b955ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
36 ------------
1b5bd3b955ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
37
1b5bd3b955ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
38 Rscript for calculating average PolII occupancy and FDR for RNA Pol II DamID datasets, based on original algorithms developed by Tony Southall.
1b5bd3b955ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
39 The script processes datafiles in gatc.bedgraph or gatc.gff format, such as those generated by damidseq_pipeline.
1b5bd3b955ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
40
1b5bd3b955ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
41 Differences between RNA pol II DamID and RNAseq
1b5bd3b955ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
42 -----------------------------------------------
1b5bd3b955ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
43 Although both are methods for transcriptional profiling, please be aware that there may be differences between these two methods. In particular, transcript abundancy as assessed through RNAseq will depend on transcript stability, whereas RNA pol II occupancy may provide a better indication of transcription levels.
1b5bd3b955ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
44
1b5bd3b955ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
45
1b5bd3b955ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
46 ]]></help>
1b5bd3b955ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
47 <citations>
1b5bd3b955ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
48 <citation type="doi">10.1093/bioinformatics/btv386</citation>
1b5bd3b955ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
49 </citations>
1b5bd3b955ed planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/damidseq_polII_gene_call commit 2e97fdaeafdafe2c63588de17777cd32a798adb1-dirty
mvdbeek
parents:
diff changeset
50 </tool>