| Previous changeset 3:1883d2bffd14 (2022-01-04) Next changeset 5:de26b312c0d2 (2023-06-16) |
|
Commit message:
planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 84c463c8317d7c16c2b86b1d8657932cc0f39791 |
|
modified:
proteinortho_macros.xml proteinortho_summary.xml |
| b |
| diff -r 1883d2bffd14 -r 9b67a50799e9 proteinortho_macros.xml --- a/proteinortho_macros.xml Tue Jan 04 18:45:05 2022 +0000 +++ b/proteinortho_macros.xml Tue Nov 22 16:50:38 2022 +0000 |
| b |
| @@ -1,7 +1,7 @@ <?xml version="1.0"?> <macros> - <token name="@TOOL_VERSION@">6.0.32</token> - <token name="@WRAPPER_VERSION@">0</token> + <token name="@TOOL_VERSION@">6.1.2</token> + <token name="@WRAPPER_VERSION@">1</token> <token name="@PROFILE@">20.09</token> <xml name="citations"> <citations> @@ -14,10 +14,10 @@ <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="2.0.9">diamond</requirement> - <requirement type="package" version="2.12.0">blast</requirement> - <requirement type="package" version="36">blat</requirement> - <requirement type="package" version="1257">last</requirement> + <requirement type="package" version="2.0.15">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> </requirements> </xml> <xml name="version_command"> |
| b |
| diff -r 1883d2bffd14 -r 9b67a50799e9 proteinortho_summary.xml --- a/proteinortho_summary.xml Tue Jan 04 18:45:05 2022 +0000 +++ b/proteinortho_summary.xml Tue Nov 22 16:50:38 2022 +0000 |
| [ |
| @@ -6,27 +6,33 @@ <expand macro="requirements"/> <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 $queryfile2: '$queryfile2' #end if - 2>&1 | awk '/^$/ && !f{f=1;next}1' | awk -v RS= '{print > ("output" NR ".tsv")}' + 2>&1 + | awk '/^$/ && !f{f=1;next}1' ## remove potentially present 1st empty line + | awk 'BEGIN{i=0} /^$/{i+=1}{print > ("output" i ".tsv")}' ## split file at empty lines && - mv output1.tsv adjacencyMat.tsv && - mv output2.tsv average1paths.tsv && - mv output3.tsv adjacencyMatSquared.tsv && - mv output4.tsv average2paths.tsv + mv output1.tsv '$adjacencyMat' && + mv output2.tsv '$average1paths' && + mv output3.tsv '$adjacencyMatSquared' && + mv output4.tsv '$average2paths' ]]></command> <inputs> <param name="queryfile" type="data" format="tabular" label="A orthology-pairs / RBH file"/> <param name="queryfile2" type="data" format="tabular" optional="true" label="(optional) A second orthology-pairs / RBH file" help="If you provide a second file, then difference is calculated (GRAPH - second GRAPH)"/> </inputs> <outputs> - <data name="adjacencyMat" format="tabular" label="${tool.name} on ${on_string}: Adjacency Matrix" from_work_dir="adjacencyMat.tsv"/> - <data name="average1paths" format="tabular" label="${tool.name} on ${on_string}: Average number of Edges" from_work_dir="average1paths.tsv"/> - <data name="adjacencyMatSquared" format="tabular" label="${tool.name} on ${on_string}: Matrix of 2-paths" from_work_dir="adjacencyMatSquared.tsv"/> - <data name="average2paths" format="tabular" label="${tool.name} on ${on_string}: Average number of 2-paths" from_work_dir="average2paths.tsv"/> + <data name="adjacencyMat" format="tabular" label="${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"> @@ -35,24 +41,28 @@ <assert_contents> <has_text text="18"/> <has_text text="14"/> + <has_text text="TERM" negate="true"/> </assert_contents> </output> <output name="average1paths"> <assert_contents> <has_text text="9.6"/> <has_text text="15"/> + <has_text text="TERM" negate="true"/> </assert_contents> </output> <output name="adjacencyMatSquared"> <assert_contents> <has_text text="750"/> <has_text text="74"/> + <has_text text="TERM" negate="true"/> </assert_contents> </output> <output name="average2paths"> <assert_contents> <has_text text="1088.8"/> <has_text text="1374.2"/> + <has_text text="TERM" negate="true"/> </assert_contents> </output> </test> @@ -63,6 +73,7 @@ <assert_contents> <has_text text="49.6"/> <has_text text="59.8"/> + <has_text text="TERM" negate="true"/> </assert_contents> </output> </test> |