Mercurial > repos > immport-devteam > extract_fcs_keywords

annotate extractKeywords.xml @ 1:1d5e530c8a5e 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/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"
author azomics
date Mon, 22 Jun 2020 17:22:21 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
1d5e530c8a5e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"
azomics
parents:
diff changeset
1 <tool id="extract_fcs_keywords" name="Extract keywords" version="1.0+galaxy1">
1d5e530c8a5e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"
azomics
parents:
diff changeset
2 <description>from FCS files</description>
1d5e530c8a5e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"
azomics
parents:
diff changeset
3 <requirements>
1d5e530c8a5e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"
azomics
parents:
diff changeset
4 <requirement type="package" version="1.42.0">bioconductor-flowcore</requirement>
1d5e530c8a5e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"
azomics
parents:
diff changeset
5 </requirements>
1d5e530c8a5e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"
azomics
parents:
diff changeset
6 <stdio>
1d5e530c8a5e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"
azomics
parents:
diff changeset
7 <exit_code range="1:" />
1d5e530c8a5e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"
azomics
parents:
diff changeset
8 </stdio>
1d5e530c8a5e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"
azomics
parents:
diff changeset
9 <command><![CDATA[
1d5e530c8a5e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"
azomics
parents:
diff changeset
10 Rscript $__tool_directory__/FCSKeyword.R '${input}' '${keyword_file}'
1d5e530c8a5e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"
azomics
parents:
diff changeset
11 ]]>
1d5e530c8a5e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"
azomics
parents:
diff changeset
12 </command>
1d5e530c8a5e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"
azomics
parents:
diff changeset
13 <inputs>
1d5e530c8a5e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"
azomics
parents:
diff changeset
14 <param format="fcs" name="input" type="data" label="FCS file"/>
1d5e530c8a5e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"
azomics
parents:
diff changeset
15 </inputs>
1d5e530c8a5e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"
azomics
parents:
diff changeset
16 <outputs>
1d5e530c8a5e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"
azomics
parents:
diff changeset
17 <data format="tabular" name="keyword_file" label="Extract Keywords on ${input.name}"/>
1d5e530c8a5e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"
azomics
parents:
diff changeset
18 </outputs>
1d5e530c8a5e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"
azomics
parents:
diff changeset
19 <tests>
1d5e530c8a5e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"
azomics
parents:
diff changeset
20 <test>
1d5e530c8a5e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"
azomics
parents:
diff changeset
21 <param name="input" value="testfcs1.fcs"/>
1d5e530c8a5e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"
azomics
parents:
diff changeset
22 <output name="keyword_file" file="out.tabular" lines_diff="2"/>
1d5e530c8a5e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"
azomics
parents:
diff changeset
23 </test>
1d5e530c8a5e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"
azomics
parents:
diff changeset
24 </tests>
1d5e530c8a5e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"
azomics
parents:
diff changeset
25 <help><![CDATA[
1d5e530c8a5e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"
azomics
parents:
diff changeset
26 This tool extracts the Keywords from a FCS file.
1d5e530c8a5e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"
azomics
parents:
diff changeset
27
1d5e530c8a5e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"
azomics
parents:
diff changeset
28 -----
1d5e530c8a5e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"
azomics
parents:
diff changeset
29
1d5e530c8a5e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"
azomics
parents:
diff changeset
30 **Input files**
1d5e530c8a5e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"
azomics
parents:
diff changeset
31
1d5e530c8a5e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"
azomics
parents:
diff changeset
32 This tool uses FCS files as input.
1d5e530c8a5e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"
azomics
parents:
diff changeset
33
1d5e530c8a5e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"
azomics
parents:
diff changeset
34 **Output file**
1d5e530c8a5e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"
azomics
parents:
diff changeset
35
1d5e530c8a5e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"
azomics
parents:
diff changeset
36 The list of FCS file headers is output.
1d5e530c8a5e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"
azomics
parents:
diff changeset
37
1d5e530c8a5e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"
azomics
parents:
diff changeset
38 -----
1d5e530c8a5e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"
azomics
parents:
diff changeset
39
1d5e530c8a5e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"
azomics
parents:
diff changeset
40 **Example**
1d5e530c8a5e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"
azomics
parents:
diff changeset
41
1d5e530c8a5e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"
azomics
parents:
diff changeset
42 FCSversion=2
1d5e530c8a5e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"
azomics
parents:
diff changeset
43
1d5e530c8a5e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"
azomics
parents:
diff changeset
44 $BYTEORD=4,3,2,1
1d5e530c8a5e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"
azomics
parents:
diff changeset
45
1d5e530c8a5e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"
azomics
parents:
diff changeset
46 $DATATYPE=I
1d5e530c8a5e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"
azomics
parents:
diff changeset
47
1d5e530c8a5e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"
azomics
parents:
diff changeset
48 $NEXTDATA=0
1d5e530c8a5e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"
azomics
parents:
diff changeset
49
1d5e530c8a5e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"
azomics
parents:
diff changeset
50 $SYS=Macintosh System Software 9.2.2
1d5e530c8a5e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"
azomics
parents:
diff changeset
51
1d5e530c8a5e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"
azomics
parents:
diff changeset
52 CREATOR=CELLQuest 3.3
1d5e530c8a5e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"
azomics
parents:
diff changeset
53
1d5e530c8a5e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"
azomics
parents:
diff changeset
54 $TOT=20000
1d5e530c8a5e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"
azomics
parents:
diff changeset
55
1d5e530c8a5e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"
azomics
parents:
diff changeset
56 $MODE=L
1d5e530c8a5e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"
azomics
parents:
diff changeset
57
1d5e530c8a5e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"
azomics
parents:
diff changeset
58 $PAR=6
1d5e530c8a5e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"
azomics
parents:
diff changeset
59
1d5e530c8a5e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"
azomics
parents:
diff changeset
60 $P1N=FSC-H
1d5e530c8a5e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"
azomics
parents:
diff changeset
61
1d5e530c8a5e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"
azomics
parents:
diff changeset
62 .
1d5e530c8a5e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"
azomics
parents:
diff changeset
63
1d5e530c8a5e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"
azomics
parents:
diff changeset
64 ..
1d5e530c8a5e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"
azomics
parents:
diff changeset
65
1d5e530c8a5e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"
azomics
parents:
diff changeset
66 ...
1d5e530c8a5e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"
azomics
parents:
diff changeset
67 ]]>
1d5e530c8a5e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"
azomics
parents:
diff changeset
68 </help>
1d5e530c8a5e "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_fcs_keywords commit f0a40d58aec0a657b60df338c79dc1ee8e510aa0"
azomics
parents:
diff changeset
69 </tool>