| Previous changeset 1:c28c2e680bf5 (2020-06-22) |
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Commit message:
"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/fcs_gate_trans commit 88c38ff89e9e7acff592b84e0e53a8bac58623cf" |
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modified:
FCSGateTrans.xml |
| b |
| diff -r c28c2e680bf5 -r 66a54e77aa33 FCSGateTrans.xml --- a/FCSGateTrans.xml Mon Jun 22 20:30:34 2020 -0400 +++ b/FCSGateTrans.xml Mon Jul 06 19:39:35 2020 -0400 |
| [ |
| @@ -1,13 +1,20 @@ -<tool id="fcs_gate_trans_convert" name="Transform FCS data" version="1.2+galaxy0"> +<tool id="fcs_gate_trans_convert" name="Transform FCS data" version="1.2+galaxy1" profile="18.01"> <description>with optional compensation and automated gating with flowDensity.</description> <requirements> <requirement type="package" version="1.10.0">bioconductor-flowdensity</requirement> + <requirement type="package" version="1.42.0">bioconductor-flowcore</requirement> </requirements> <stdio> - <exit_code range="2:" level="fatal" description="See stderr for more details." /> + <exit_code range="1:" level="fatal" description="See stderr for more details." /> </stdio> <command><![CDATA[ - Rscript $__tool_directory__/FCSGateTrans.R '${input}' '${output}' $comp '${outformat}' '${graph}' '${report}' '${transform.trans_method}' + Rscript $__tool_directory__/FCSGateTrans.R '${input}' '${output}' $comp '${outformat}' + #if $gate + '${graph}' '${report}' + #else + 'None' 'None' + #end if + '${transform.trans_method}' #if $transform.trans_method == "arcsinh" $transform.scaling_factor #else if $transform.trans_method == "logicle" @@ -39,10 +46,6 @@ </param> </when> </conditional> - <param name="gate" type="select" label="Automatically gate debris?"> - <option value="FALSE">No, thank you</option> - <option value="TRUE">Yes, please</option> - </param> <param name="gate" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Automatically gate debris?"/> <param name="outformat" type="select" label="Output Format"> <option value="flowtext">Text File</option> @@ -67,6 +70,68 @@ <tests> <test> <param name="input" value="testfcs1.fcs"/> + <param name="comp" value="FALSE"/> + <param name="gate" value="FALSE"/> + <param name="outformat" value="flowtext"/> + <param name="trans_method" value="fcstrans"/> + <output name="output" file="nocomp.flowtext"/> + </test> + <test> + <param name="input" value="testfcs1.fcs"/> + <param name="comp" value="FALSE"/> + <param name="gate" value="FALSE"/> + <param name="outformat" value="flowtext"/> + <param name="trans_method" value="None"/> + <output name="output" file="notrans.flowtext"/> + </test> + <test> + <param name="input" value="testfcs1.fcs"/> + <param name="comp" value="FALSE"/> + <param name="gate" value="FALSE"/> + <param name="outformat" value="flowtext"/> + <param name="trans_method" value="arcsinh"/> + <param name="scaling_factor" value="150"/> + <output name="output" file="arcsinh150.flowtext"/> + </test> + <test> + <param name="input" value="testfcs1.fcs"/> + <param name="comp" value="TRUE"/> + <param name="gate" value="TRUE"/> + <param name="outformat" value="flowtext"/> + <param name="trans_method" value="fcstrans"/> + <output name="output" file="withcomp.flowtext"/> + </test> + <test> + <param name="input" value="testfcs1.fcs"/> + <param name="comp" value="TRUE"/> + <param name="gate" value="FALSE"/> + <param name="outformat" value="flowtext"/> + <param name="trans_method" value="logicle_auto"/> + <output name="output" file="log_auto.flowtext"/> + </test> + <test> + <param name="input" value="testfcs1.fcs"/> + <param name="comp" value="TRUE"/> + <param name="gate" value="FALSE"/> + <param name="outformat" value="flowtext"/> + <param name="trans_method" value="logicle"/> + <param name="w" value="0.4"/> + <param name="t" value="10000"/> + <param name="m" value="4.5"/> + <output name="output" file="logicle.flowtext"/> + </test> + <test> + <param name="input" value="testfcs1.fcs"/> + <param name="comp" value="TRUE"/> + <param name="gate" value="TRUE"/> + <param name="outformat" value="flowtext"/> + <param name="trans_method" value="fcstrans"/> + <output name="output" file="withcomp.flowtext"/> + <output name="graph" file="graph.png" compare="sim_size"/> + <output name="report" file="report.txt"/> + </test> + <test> + <param name="input" value="testfcs1.fcs"/> <param name="comp" value="TRUE"/> <param name="gate" value="FALSE"/> <param name="outformat" value="FCS"/> @@ -89,16 +154,15 @@ **Input files** -This tool uses FCS files as input and files are processed serially. Users choose to automatically gate cellular debris, and/or compensate the data. +This tool uses FCS files as input and files are processed serially. Users choose which transformation algorithm to apply, and whether to automatically gate cellular debris, and/or compensate the data. **Output files** -Output is tab-separated text containing transformed fluorescence intensity values for each marker. -If the option is selected, a FCS file (format FCS3.0) is generated. +Output is a table of fluorescence intensity values for each marker, as a text file, FCS3.0 or R Object (flowFrame). **Gating output** -Automatically gated output includes a summary of data pre- and post-gating as well as density scatter plots pre- and post- gating for each marker pair. +Automatically gated output includes a summary of data pre- and post-gating as well as density scatter plots pre- and post- gating for each marker pair. Please check to make sure the gating is doing what you think it should be doing. ----- |