Mercurial > repos > iuc > proteinortho_summary
comparison proteinortho_summary.xml @ 4:9b67a50799e9 draft
planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 84c463c8317d7c16c2b86b1d8657932cc0f39791
author | iuc |
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date | Tue, 22 Nov 2022 16:50:38 +0000 |
parents | c3f58c2eee1e |
children | de26b312c0d2 |
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3:1883d2bffd14 | 4:9b67a50799e9 |
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4 <import>proteinortho_macros.xml</import> | 4 <import>proteinortho_macros.xml</import> |
5 </macros> | 5 </macros> |
6 <expand macro="requirements"/> | 6 <expand macro="requirements"/> |
7 <expand macro="version_command"/> | 7 <expand macro="version_command"/> |
8 <command detect_errors="exit_code"><![CDATA[ | 8 <command detect_errors="exit_code"><![CDATA[ |
9 export TERM=dumb && | |
10 ## TODOs: | |
11 ## - check if 2>&1 can be removed https://gitlab.com/paulklemm_PHD/proteinortho/-/merge_requests/9 | |
12 ## - include output0.tsv as Galaxy output? | |
9 proteinortho_summary.pl | 13 proteinortho_summary.pl |
10 $queryfile | 14 $queryfile |
11 #if $queryfile2: | 15 #if $queryfile2: |
12 '$queryfile2' | 16 '$queryfile2' |
13 #end if | 17 #end if |
14 2>&1 | awk '/^$/ && !f{f=1;next}1' | awk -v RS= '{print > ("output" NR ".tsv")}' | 18 2>&1 |
19 | awk '/^$/ && !f{f=1;next}1' ## remove potentially present 1st empty line | |
20 | awk 'BEGIN{i=0} /^$/{i+=1}{print > ("output" i ".tsv")}' ## split file at empty lines | |
15 && | 21 && |
16 mv output1.tsv adjacencyMat.tsv && | 22 mv output1.tsv '$adjacencyMat' && |
17 mv output2.tsv average1paths.tsv && | 23 mv output2.tsv '$average1paths' && |
18 mv output3.tsv adjacencyMatSquared.tsv && | 24 mv output3.tsv '$adjacencyMatSquared' && |
19 mv output4.tsv average2paths.tsv | 25 mv output4.tsv '$average2paths' |
20 ]]></command> | 26 ]]></command> |
21 <inputs> | 27 <inputs> |
22 <param name="queryfile" type="data" format="tabular" label="A orthology-pairs / RBH file"/> | 28 <param name="queryfile" type="data" format="tabular" label="A orthology-pairs / RBH file"/> |
23 <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)"/> | 29 <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)"/> |
24 </inputs> | 30 </inputs> |
25 <outputs> | 31 <outputs> |
26 <data name="adjacencyMat" format="tabular" label="${tool.name} on ${on_string}: Adjacency Matrix" from_work_dir="adjacencyMat.tsv"/> | 32 <data name="adjacencyMat" format="tabular" label="${tool.name} on ${on_string}: Adjacency Matrix"/> |
27 <data name="average1paths" format="tabular" label="${tool.name} on ${on_string}: Average number of Edges" from_work_dir="average1paths.tsv"/> | 33 <data name="average1paths" format="tabular" label="${tool.name} on ${on_string}: Average number of Edges"/> |
28 <data name="adjacencyMatSquared" format="tabular" label="${tool.name} on ${on_string}: Matrix of 2-paths" from_work_dir="adjacencyMatSquared.tsv"/> | 34 <data name="adjacencyMatSquared" format="tabular" label="${tool.name} on ${on_string}: Matrix of 2-paths"/> |
29 <data name="average2paths" format="tabular" label="${tool.name} on ${on_string}: Average number of 2-paths" from_work_dir="average2paths.tsv"/> | 35 <data name="average2paths" format="tabular" label="${tool.name} on ${on_string}: Average number of 2-paths"/> |
30 </outputs> | 36 </outputs> |
31 <tests> | 37 <tests> |
32 <test expect_num_outputs="4"> | 38 <test expect_num_outputs="4"> |
33 <param name="queryfile" value="result.proteinortho-graph"/> | 39 <param name="queryfile" value="result.proteinortho-graph"/> |
34 <output name="adjacencyMat"> | 40 <output name="adjacencyMat"> |
35 <assert_contents> | 41 <assert_contents> |
36 <has_text text="18"/> | 42 <has_text text="18"/> |
37 <has_text text="14"/> | 43 <has_text text="14"/> |
44 <has_text text="TERM" negate="true"/> | |
38 </assert_contents> | 45 </assert_contents> |
39 </output> | 46 </output> |
40 <output name="average1paths"> | 47 <output name="average1paths"> |
41 <assert_contents> | 48 <assert_contents> |
42 <has_text text="9.6"/> | 49 <has_text text="9.6"/> |
43 <has_text text="15"/> | 50 <has_text text="15"/> |
51 <has_text text="TERM" negate="true"/> | |
44 </assert_contents> | 52 </assert_contents> |
45 </output> | 53 </output> |
46 <output name="adjacencyMatSquared"> | 54 <output name="adjacencyMatSquared"> |
47 <assert_contents> | 55 <assert_contents> |
48 <has_text text="750"/> | 56 <has_text text="750"/> |
49 <has_text text="74"/> | 57 <has_text text="74"/> |
58 <has_text text="TERM" negate="true"/> | |
50 </assert_contents> | 59 </assert_contents> |
51 </output> | 60 </output> |
52 <output name="average2paths"> | 61 <output name="average2paths"> |
53 <assert_contents> | 62 <assert_contents> |
54 <has_text text="1088.8"/> | 63 <has_text text="1088.8"/> |
55 <has_text text="1374.2"/> | 64 <has_text text="1374.2"/> |
65 <has_text text="TERM" negate="true"/> | |
56 </assert_contents> | 66 </assert_contents> |
57 </output> | 67 </output> |
58 </test> | 68 </test> |
59 <test expect_num_outputs="4"> | 69 <test expect_num_outputs="4"> |
60 <param name="queryfile" value="result.proteinortho-graph"/> | 70 <param name="queryfile" value="result.proteinortho-graph"/> |
61 <param name="queryfile2" value="result.blast-graph"/> | 71 <param name="queryfile2" value="result.blast-graph"/> |
62 <output name="average2paths"> | 72 <output name="average2paths"> |
63 <assert_contents> | 73 <assert_contents> |
64 <has_text text="49.6"/> | 74 <has_text text="49.6"/> |
65 <has_text text="59.8"/> | 75 <has_text text="59.8"/> |
76 <has_text text="TERM" negate="true"/> | |
66 </assert_contents> | 77 </assert_contents> |
67 </output> | 78 </output> |
68 </test> | 79 </test> |
69 </tests> | 80 </tests> |
70 <help><![CDATA[proteinortho summary | 81 <help><![CDATA[proteinortho summary |