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Commit message:
planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit b4d8b8da2a259973c9ad90e4b9d1a3e22ae4348f |
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modified:
proteinortho_macros.xml proteinortho_summary.xml |
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| diff -r 9b67a50799e9 -r de26b312c0d2 proteinortho_macros.xml --- a/proteinortho_macros.xml Tue Nov 22 16:50:38 2022 +0000 +++ b/proteinortho_macros.xml Fri Jun 16 20:52:56 2023 +0000 |
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| @@ -1,6 +1,6 @@ <?xml version="1.0"?> <macros> - <token name="@TOOL_VERSION@">6.1.2</token> + <token name="@TOOL_VERSION@">6.2.3</token> <token name="@WRAPPER_VERSION@">1</token> <token name="@PROFILE@">20.09</token> <xml name="citations"> @@ -12,12 +12,10 @@ <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">proteinortho</requirement> - <!-- blast, blat, and last are not in the biopython requirements - diamond is, but latest version does not work: https://gitlab.com/paulklemm_PHD/proteinortho/-/issues/55 --> - <requirement type="package" version="2.0.15">diamond</requirement> + <requirement type="package" version="2.1.4">diamond</requirement> <requirement type="package" version="2.13.0">blast</requirement> <requirement type="package" version="377">ucsc-blat</requirement> - <requirement type="package" version="1418">last</requirement> + <requirement type="package" version="1422">last</requirement> </requirements> </xml> <xml name="version_command"> |
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| diff -r 9b67a50799e9 -r de26b312c0d2 proteinortho_summary.xml --- a/proteinortho_summary.xml Tue Nov 22 16:50:38 2022 +0000 +++ b/proteinortho_summary.xml Fri Jun 16 20:52:56 2023 +0000 |
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| @@ -7,9 +7,6 @@ <expand macro="version_command"/> <command detect_errors="exit_code"><![CDATA[ export TERM=dumb && - ## TODOs: - ## - check if 2>&1 can be removed https://gitlab.com/paulklemm_PHD/proteinortho/-/merge_requests/9 - ## - include output0.tsv as Galaxy output? proteinortho_summary.pl $queryfile #if $queryfile2: @@ -19,6 +16,7 @@ | awk '/^$/ && !f{f=1;next}1' ## remove potentially present 1st empty line | awk 'BEGIN{i=0} /^$/{i+=1}{print > ("output" i ".tsv")}' ## split file at empty lines && + mv output0.tsv '$distribution' && mv output1.tsv '$adjacencyMat' && mv output2.tsv '$average1paths' && mv output3.tsv '$adjacencyMatSquared' && @@ -29,14 +27,20 @@ <param name="queryfile2" type="data" format="tabular" optional="true" label="(optional) A second orthology-pairs / RBH file" help="If you provide a second file, then difference is calculated (GRAPH - second GRAPH)"/> </inputs> <outputs> + <data name="distribution" format="tabular" label="${tool.name} on ${on_string}: Protein-Group distribution"/> <data name="adjacencyMat" format="tabular" label="${tool.name} on ${on_string}: Adjacency Matrix"/> <data name="average1paths" format="tabular" label="${tool.name} on ${on_string}: Average number of Edges"/> <data name="adjacencyMatSquared" format="tabular" label="${tool.name} on ${on_string}: Matrix of 2-paths"/> <data name="average2paths" format="tabular" label="${tool.name} on ${on_string}: Average number of 2-paths"/> </outputs> <tests> - <test expect_num_outputs="4"> + <test expect_num_outputs="5"> <param name="queryfile" value="result.proteinortho-graph"/> + <output name="distribution"> + <assert_contents> + <has_text text="%"/> + </assert_contents> + </output> <output name="adjacencyMat"> <assert_contents> <has_text text="18"/> @@ -66,7 +70,7 @@ </assert_contents> </output> </test> - <test expect_num_outputs="4"> + <test expect_num_outputs="5"> <param name="queryfile" value="result.proteinortho-graph"/> <param name="queryfile2" value="result.blast-graph"/> <output name="average2paths"> @@ -77,6 +81,15 @@ </assert_contents> </output> </test> + <test expect_num_outputs="5"> + <param name="queryfile" value="result.blast-graph"/> + <output name="average2paths"> + <assert_contents> + <has_text text="115.2"/> + <has_text text="TERM" negate="true"/> + </assert_contents> + </output> + </test> </tests> <help><![CDATA[proteinortho summary @@ -84,6 +97,8 @@ proteinortho_summary : Summaries the (orthology-pairs/RBH) file(s) to determine how well the species are connected to each other. + * **Protein-Group distribution** (for orthology-pairs) : This report contains overal statistics about the output. (i) Number of groups that contains at least p% input species (with p ranging between 0 and 100). (ii) number of groups for each input species. + * **Adjacency Matrix** : How well are the species connected to each other directly. * **Average number of Edges** : Averaged number of connections for each species. @@ -92,7 +107,6 @@ * **Average number of 2-paths** : The average number of 2-paths for each species. If a species is not well connected to all the other species, it will result in a low average. - If you supply a second orthology-pairs/RBH then the difference is calculated for all 4 outputs. E.g. given the RBH and the orthology-pairs of the same run : The outputs show how much the clustering removed from the initial reciprocal best hit graph. |