Mercurial > repos > galaxyp > pepquery2
changeset 6:01fd80b15053 draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pepquery2 commit 00e1b1770d0b1f9fe31384b37b55f7ae9d97b597
author | galaxyp |
---|---|
date | Sun, 06 Nov 2022 16:23:05 +0000 |
parents | 2045f3b68773 |
children | |
files | pepquery2.tar.gz pepquery2.xml |
diffstat | 2 files changed, 9 insertions(+), 28 deletions(-) [+] |
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--- a/pepquery2.xml Mon Oct 31 14:41:50 2022 +0000 +++ b/pepquery2.xml Sun Nov 06 16:23:05 2022 +0000 @@ -165,11 +165,7 @@ <option value="peptide">peptide</option> <option value="protein">protein</option> <option value="DNA">DNA (translate to protein sequences)</option> - <!-- these are not working with pepquery version 1.6 - <option value="3">VCF (translate to protein sequences)</option> - <option value="4">BED (translate to protein sequences)</option> - <option value="5">GTF (translate to protein sequences)</option> - --> + <!-- VCF,BED,GTF input options have not been implemented in this tool --> </param> <when value="peptide"> <conditional name="multiple"> @@ -231,20 +227,6 @@ <option value="6">6</option> </param> </when> - <!-- these are not working with pepquery version 1.6 - <when value="3"> - <param name="input" type="data" format="vcf" label="VCF File" argument="-i" help="" /> - <param name="anno" type="data_collection" label="Annotation Files" argument="-anno" help="Annotation files for the VCF file. Please follow preparation instructions here: http://bioconductor.org/packages/devel/bioc/html/PGA.html" /> - </when> - <when value="4"> - <param name="input" type="data" format="bed" label="BED File" argument="-i" help="" /> - <param name="anno" type="data_collection" label="Annotation Files" argument="-anno" help="Annotation files for the BED file. Please follow preparation instructions here: http://bioconductor.org/packages/devel/bioc/html/PGA.html" /> - </when> - <when value="5"> - <param name="input" type="data" format="gtf" label="GTF File" argument="-i" help="" /> - <param name="anno" type="data_collection" label="Annotation Files" argument="-anno" help="Annotation files for the GTF file. Please follow preparation instructions here: http://bioconductor.org/packages/devel/bioc/html/PGA.html" /> - </when> - --> </conditional> <conditional name="db_type"> <param name="db_type_selector" type="select" label="Protein Reference Database from" help="" > @@ -454,7 +436,7 @@ </outputs> <tests> <!-- Test-1 PepQueryDB peptide gencode:human --> - <test> + <test expect_num_outputs="2"> <conditional name="validation"> <param name="task_type" value="novel"/> </conditional> @@ -513,6 +495,7 @@ <has_text text="LVVVGADGVGK" /> <not_has_text text="AHSSMVGVNLPQK" /> <has_text text="02CPTAC_LUAD_W_BI_20180518_KR_f15:25149:2" /> + <has_n_columns n="22" /> </assert_contents> </output> <output name="log_txt"> @@ -523,7 +506,7 @@ </test> <!-- Test-2 PepQueryDB peptide gencode:human pep.txt --> - <test> + <test expect_num_outputs="2"> <conditional name="validation"> <param name="task_type" value="novel"/> </conditional> @@ -582,6 +565,7 @@ <has_text text="LVVVGADGVGK" /> <not_has_text text="AHSSMVGVNLPQK" /> <has_text text="02CPTAC_LUAD_W_BI_20180518_KR_f15:25149:2" /> + <has_n_columns n="22" /> </assert_contents> </output> <output name="log_txt"> @@ -592,7 +576,7 @@ </test> <!-- Test-3 MGF peptide Uniprot.fasta --> - <test> + <test expect_num_outputs="2"> <conditional name="validation"> <param name="task_type" value="novel"/> </conditional> @@ -652,18 +636,14 @@ <output name="psm_rank_txt"> <assert_contents> <has_text text="ELGSSDLTAR" /> - </assert_contents> - </output> - <output name="psm_rank_txt"> - <assert_contents> - <has_text text="ELGSSDLTAR" /> <has_line_matching expression="ELGSSDLTAR\tiTRAQ 4-plex of peptide N-term@0\[144.1\d+\]\t2\tiTRAQ_f4:3:2\t2\t1191.62\d+\t-3.04\d+\t-0.003\d+\t0.0\t1191.6\d+\t596.8\d+\t24.1\d+\t0\t0\t1\t995\t0.002\d+\t1\t0\tYes\t24.1\d+\t24.1\d+"/> + <has_n_columns n="22" /> </assert_contents> </output> </test> <!-- Test-4 PepQueryDB known peptide gencode:human pep.txt --> - <test> + <test expect_num_outputs="2"> <conditional name="validation"> <param name="task_type" value="known"/> </conditional> @@ -692,6 +672,7 @@ <assert_contents> <has_text text="AHSSMVGVNLPQK" /> <has_text text="6CPTAC_LUAD_W_BI_20180718_KL_f12:20286:3" /> + <has_n_columns n="22" /> </assert_contents> </output> </test>