Mercurial > repos > iuc > mageck_test
diff mageck_test.xml @ 4:38073c236d71 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mageck commit 4478aabdcb10e4787450b1b23944defa7dc38ffe
| author | iuc |
|---|---|
| date | Mon, 04 Jun 2018 10:58:16 -0400 |
| parents | 81bbbddcf285 |
| children | 9b4f4533c9ee |
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--- a/mageck_test.xml Thu Apr 19 05:35:12 2018 -0400 +++ b/mageck_test.xml Mon Jun 04 10:58:16 2018 -0400 @@ -160,8 +160,18 @@ <param name="count_table" value="in.test.sample.txt" ftype="tabular" /> <param name="treatment_id" value="HL60_final,KBM7_final" /> <param name="control_id" value="HL60_initial,KBM7_initial" /> - <output name="gene_summary" file="out.test.gene_summary.txt"/> - <output name="sgrna_summary" file="out.test.sgrna_summary.txt"/> + <output name="gene_summary"> + <assert_contents> + <has_text_matching expression="id\tnum\tneg|score\tneg|p-value\tneg|fdr\tneg|rank\tneg|goodsgrna\tneg|lfc\tpos|score\tpos|p-value\tpos|fdr\tpos|rank\tpos|goodsgrna\tpos|lfc" /> + <has_text_matching expression="ACD.*10.*0.9996.*-0.0296" /> + </assert_contents> + </output> + <output name="sgrna_summary"> + <assert_contents> + <has_text_matching expression="sgrna\tGene\tcontrol_count\ttreatment_count\tcontrol_mean\ttreat_mean\tLFC\tcontrol_var\tadj_var\tscore\tp.low\tp.high\tp.twosided\tFDR\thigh_in_treatment" /> + <has_text_matching expression="ADCK3_m227149144.*ADCK3.*263.11.*189.27.*False" /> + </assert_contents> + </output> </test> <!-- Ensure MAGeCK's additional outputs works --> <test expect_num_outputs="7"> @@ -172,13 +182,35 @@ <param name="normcounts" value="True" /> <param name="pdfreport" value="True" /> <param name="rfilesOpt" value="True" /> - <output name="gene_summary" file="out.test.gene_summary.txt"/> - <output name="sgrna_summary" file="out.test.sgrna_summary.txt"/> + <output name="gene_summary"> + <assert_contents> + <has_text_matching expression="id\tnum\tneg|score\tneg|p-value\tneg|fdr\tneg|rank\tneg|goodsgrna\tneg|lfc\tpos|score\tpos|p-value\tpos|fdr\tpos|rank\tpos|goodsgrna\tpos|lfc" /> + <has_text_matching expression="ACD.*10.*0.9996.*-0.0296" /> + </assert_contents> + </output> + <output name="sgrna_summary"> + <assert_contents> + <has_text_matching expression="sgrna\tGene\tcontrol_count\ttreatment_count\tcontrol_mean\ttreat_mean\tLFC\tcontrol_var\tadj_var\tscore\tp.low\tp.high\tp.twosided\tFDR\thigh_in_treatment" /> + <has_text_matching expression="ADCK3_m227149144.*ADCK3.*263.11.*189.27.*False" /> + </assert_contents> + </output> + <output name="log"> + <assert_contents> + <has_text_matching expression="Welcome to MAGeCK" /> + </assert_contents> + </output> + <output name="rscript"> + <assert_contents> + <has_text_matching expression="output_summary.tex" /> + </assert_contents> + </output> + <output name="rnwfile"> + <assert_contents> + <has_text_matching expression="This is a template file for Sweave used in MAGeCK" /> + </assert_contents> + </output> + <output name="plots" file="out.test.plots.pdf" compare="sim_size"/> <output name="normcounts" file="out.test.normalized.txt"/> - <output name="log" file="out.test.log.txt" compare="sim_size"/> - <output name="plots" file="out.test.plots.pdf" compare="sim_size"/> - <output name="rscript" file="out.test.R" /> - <output name="rnwfile" file="output_summary.Rnw" /> </test> </tests>