Mercurial > repos > azomics > check_fcs_header
comparison getFCSheaders.xml @ 0:2227def10ea4 draft default tip
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_fcs_headers commit 6da41781e60ad4e264c4d725c5373b099b4766d4"
| author | azomics |
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| date | Wed, 24 Jun 2020 17:36:27 -0400 |
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| -1:000000000000 | 0:2227def10ea4 |
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| 1 <tool id="get_fcs_headers" name="Get list of markers" version="2.0+galaxy0"> | |
| 2 <description>in FCS files.</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="1.42.0">bioconductor-flowcore</requirement> | |
| 5 </requirements> | |
| 6 <stdio> | |
| 7 <exit_code range="10" level="warning" description="Not all files are valid FCS files, see output for details." /> | |
| 8 </stdio> | |
| 9 <command><![CDATA[ | |
| 10 Rscript '$__tool_directory__/getFCSheader.R' '${output_file}' | |
| 11 #for $f in $input | |
| 12 '${f}' '${f.name}' | |
| 13 #end for | |
| 14 ]]> | |
| 15 </command> | |
| 16 <inputs> | |
| 17 <param format="fcs" name="input" type="data_collection" collection_type="list" label="FCS files Collection"/> | |
| 18 </inputs> | |
| 19 <outputs> | |
| 20 <data format="tabular" name="output_file" label="Headers of files in ${input.name}"/> | |
| 21 </outputs> | |
| 22 <tests> | |
| 23 <test> | |
| 24 <param name="input"> | |
| 25 <collection type="list"> | |
| 26 <element name="input1.fcs" value="input1.fcs"/> | |
| 27 <element name="input2.fcs" value="input2.fcs"/> | |
| 28 <element name="input3.fcs" value="input3.fcs"/> | |
| 29 </collection> | |
| 30 </param> | |
| 31 <output name="output_file" file="output.tabular" lines_diff="8"/> | |
| 32 </test> | |
| 33 </tests> | |
| 34 <help><![CDATA[ | |
| 35 This tool returns a table of the headers of a set of FCS files. | |
| 36 | |
| 37 ----- | |
| 38 | |
| 39 **Input files** | |
| 40 | |
| 41 This tool requires collections of FCS files as input. | |
| 42 | |
| 43 **Output file** | |
| 44 | |
| 45 The output file is a table listing the markers and channels for each file. | |
| 46 | |
| 47 ----- | |
| 48 | |
| 49 **Example** | |
| 50 | |
| 51 *File1*:: | |
| 52 | |
| 53 Marker1 Marker2 Marker3 | |
| 54 34 45 12 | |
| 55 33 65 10 | |
| 56 | |
| 57 *File2*:: | |
| 58 | |
| 59 Marker4 Marker5 Marker3 | |
| 60 19 62 98 | |
| 61 12 36 58 | |
| 62 | |
| 63 *Output*:: | |
| 64 | |
| 65 Filename Index 1 2 3 | |
| 66 File1 channels Channel1 Channel2 Channel3 | |
| 67 File2 channels Channel4 Channel5 Channel3 | |
| 68 File1 markers Marker1 Marker2 Marker3 | |
| 69 File2 markers Marker4 Marker5 Marker3 | |
| 70 ]]> | |
| 71 </help> | |
| 72 </tool> |