Mercurial > repos > azomics > flowtext_summary
comparison FCSstats_text.xml @ 0:2916b895840f draft default tip
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/flowtext_summary commit 2a47c0c1e27462d21098006ba4fe0789b1ed37ec"
| author | azomics |
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| date | Mon, 22 Jun 2020 20:32:32 -0400 |
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| -1:000000000000 | 0:2916b895840f |
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| 1 <tool id="get_txt_fcs_stats" name="Get summary" version="1.0+galaxy1"> | |
| 2 <description>of txt-converted FCS files</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="0.17.1">pandas</requirement> | |
| 5 </requirements> | |
| 6 <stdio> | |
| 7 <exit_code range="2:" level="fatal" description="See stderr for more details." /> | |
| 8 </stdio> | |
| 9 <command><![CDATA[ | |
| 10 python '$__tool_directory__/FCSstats_txt.py' -i '${input}' -o '${output}' | |
| 11 ]]> | |
| 12 </command> | |
| 13 <inputs> | |
| 14 <param format="flowtext,txt,tabular" name="input" type="data" label="txt-converted FCS file"/> | |
| 15 </inputs> | |
| 16 <outputs> | |
| 17 <data format="tabular" name="output" label="Summary statisitics of ${input.name}"/> | |
| 18 </outputs> | |
| 19 <tests> | |
| 20 <test> | |
| 21 <param name="input" value="input.flowtext"/> | |
| 22 <output name="output" file="output.tabular"/> | |
| 23 </test> | |
| 24 </tests> | |
| 25 <help><![CDATA[ | |
| 26 This tool generates a summary of a txt-converted FCS file and list of markers. | |
| 27 | |
| 28 ----- | |
| 29 | |
| 30 **Input file** | |
| 31 | |
| 32 This tool uses txt-converted FCS files as input. | |
| 33 | |
| 34 **Output file** | |
| 35 | |
| 36 File summary includes number of events, list of markers and parameters, and summary statistics for each. | |
| 37 | |
| 38 ----- | |
| 39 | |
| 40 **Example** | |
| 41 | |
| 42 *Output*:: | |
| 43 | |
| 44 FSC SSC CD4 CCR3 CD8 CCR4 | |
| 45 mean 475.4 413.4 288.8 157.9 218.1 179.6 | |
| 46 std 165.2 390.7 199.9 117.3 201.7 95.7 | |
| 47 min 261.0 18.0 0.0 0.0 0.0 0.0 | |
| 48 25% 354.0 121.0 112.0 65.0 58.0 109.0 | |
| 49 50% 398.0 167.0 209.0 159.0 180.0 179.0 | |
| 50 75% 609.0 951.2 512.0 237.0 275.0 245.0 | |
| 51 max 1023.0 1023.0 775.0 1023.0 1023.0 841.0 | |
| 52 20000 events | |
| 53 ]]> | |
| 54 </help> | |
| 55 </tool> |