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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/psm_zscore commit 6ea2ae47fb74320afbb88a92e3fe40b5f8f86ad1
author | galaxyp |
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date | Tue, 02 May 2017 13:35:55 -0400 |
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<tool id="psm_zscore" name="PSM z-score" version="0.1.0"> <description>Add a zscore column to a PSM report</description> <requirements> <requirement type="package" version="3.2.1">R</requirement> </requirements> <stdio> <exit_code range="1:" /> </stdio> <command><![CDATA[ echo "Global FDR: "; Rscript '${__tool_directory__}/PSM_Z_Score.R' z_cutoff=$z_cutoff ppm_tolerance=$ppm_tolerance psm_report='"$psm_report"' output_psm_report='"$zscored_psm_report"' | awk '{print \$2}' ]]></command> <inputs> <param name="psm_report" type="data" format="tabular" label="PSM report"/> <param name="z_cutoff" type="float" value="2" min="0.1" max="10" label="Z-value cutoof"/> <param name="ppm_tolerance" type="integer" value="10" label="ppm tolerance" help="The ppm tolerance value used when generating the PSM report"/> </inputs> <outputs> <data name="zscored_psm_report" format="tabular" /> </outputs> <tests> <test> <param name="psm_report" ftype="tabular" value="PSM_report_in.tsv"/> <param name="z_cutoff" value="2"/> <param name="ppm_tolerance" value="0"/> <output name="zscored_psm_report"> <assert_contents> <has_text_matching expression="1\tNP_001419\t.*\t\d+\.\d+"/> </assert_contents> </output> </test> </tests> <help><![CDATA[ TODO: Fill in help. ]]></help> </tool>