Mercurial > repos > azomics > flowtext_summary
diff 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 |
|---|---|
| date | Mon, 22 Jun 2020 20:32:32 -0400 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/FCSstats_text.xml Mon Jun 22 20:32:32 2020 -0400 @@ -0,0 +1,55 @@ +<tool id="get_txt_fcs_stats" name="Get summary" version="1.0+galaxy1"> + <description>of txt-converted FCS files</description> + <requirements> + <requirement type="package" version="0.17.1">pandas</requirement> + </requirements> + <stdio> + <exit_code range="2:" level="fatal" description="See stderr for more details." /> + </stdio> + <command><![CDATA[ + python '$__tool_directory__/FCSstats_txt.py' -i '${input}' -o '${output}' + ]]> + </command> + <inputs> + <param format="flowtext,txt,tabular" name="input" type="data" label="txt-converted FCS file"/> + </inputs> + <outputs> + <data format="tabular" name="output" label="Summary statisitics of ${input.name}"/> + </outputs> + <tests> + <test> + <param name="input" value="input.flowtext"/> + <output name="output" file="output.tabular"/> + </test> + </tests> + <help><![CDATA[ + This tool generates a summary of a txt-converted FCS file and list of markers. + +----- + +**Input file** + +This tool uses txt-converted FCS files as input. + +**Output file** + +File summary includes number of events, list of markers and parameters, and summary statistics for each. + +----- + +**Example** + +*Output*:: + + FSC SSC CD4 CCR3 CD8 CCR4 + mean 475.4 413.4 288.8 157.9 218.1 179.6 + std 165.2 390.7 199.9 117.3 201.7 95.7 + min 261.0 18.0 0.0 0.0 0.0 0.0 + 25% 354.0 121.0 112.0 65.0 58.0 109.0 + 50% 398.0 167.0 209.0 159.0 180.0 179.0 + 75% 609.0 951.2 512.0 237.0 275.0 245.0 + max 1023.0 1023.0 775.0 1023.0 1023.0 841.0 + 20000 events + ]]> + </help> +</tool>