| Previous changeset 1:aef09ac6d0a5 (2019-06-24) Next changeset 3:3d86c89f15bf (2019-08-29) |
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Commit message:
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_mannwhitney_de commit 9d570db083bd51751f4784dc367ee18aa0024ecd |
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modified:
mannwhitney_de.xml |
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added:
test-data/signature_3columns.tsv |
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| diff -r aef09ac6d0a5 -r 60964af87364 mannwhitney_de.xml --- a/mannwhitney_de.xml Mon Jun 24 19:17:26 2019 -0400 +++ b/mannwhitney_de.xml Mon Jul 01 09:05:28 2019 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="mannwhitney_de" name="Perform a differential analysis" version="0.9.1"> +<tool id="mannwhitney_de" name="Perform a differential analysis" version="0.9.2"> <description>using a Mann-Whitney test</description> <requirements> <requirement type="package" version="1.3.2=r3.3.2_0">r-optparse</requirement> @@ -34,7 +34,8 @@ <option value="FALSE">No</option> </param> <param name="comparison_factor_file" type="data" format="tabular" label="Comparison factor table" - help="A tsv table file with two columns : cell identifiers and a column that split cells into two categories." /> + help="A tsv table file with two columns : cell identifiers and a column that split cells into two categories. + Other columns are ignored" /> <param name="factor1" type="text" label="Condition-1. The first level (value) that the comparison factor can take." help="typical values could be 'LOW', 'wt', 't1', etc."/> <param name="factor2" type="text" label="Condition-2. The second level (value) that the comparison factor can take." help="typical values could be 'HIGH', 'mutant', 't2', etc."/> <param name="fdr" type="float" value="0.01" label="FDR threshold" @@ -58,6 +59,17 @@ <output name="output" file="geneMetadata_log.tsv" ftype="tabular"/> </test> <test> + <param name="input" value="filtered-0.05.tab" ftype="txt"/> + <param name="sep" value="tab" /> + <param name="colnames" value="TRUE"/> + <param name="comparison_factor_file" value="signature_3columns.tsv" ftype="tabular"/> + <param name="factor1" value="LOW"/> + <param name="factor2" value="HIGH"/> + <param name="fdr" value="0.01"/> + <param name="log" value="true"/> + <output name="output" file="geneMetadata_log.tsv" ftype="tabular"/> + </test> + <test> <param name="input" value="filterCells_100.tsv" ftype="txt"/> <param name="sep" value="tab" /> <param name="colnames" value="TRUE"/> |
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| diff -r aef09ac6d0a5 -r 60964af87364 test-data/signature_3columns.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/signature_3columns.tsv Mon Jul 01 09:05:28 2019 -0400 |
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| @@ -0,0 +1,101 @@ +cells factor add_column +1001000173.B4 LOW 1001000173.B4 +1001000173.A2 LOW 1001000173.A2 +1001000173.E2 LOW 1001000173.E2 +1001000173.F6 LOW 1001000173.F6 +1001000173.B12 LOW 1001000173.B12 +1001000173.H1 HIGH 1001000173.H1 +1001000173.E4 HIGH 1001000173.E4 +1001000173.C2 LOW 1001000173.C2 +1001000173.F4 LOW 1001000173.F4 +1001000173.E10 HIGH 1001000173.E10 +1001000173.E6 LOW 1001000173.E6 +1001000173.C4 HIGH 1001000173.C4 +1001000173.B10 LOW 1001000173.B10 +1001000173.A7 LOW 1001000173.A7 +1001000173.B8 LOW 1001000173.B8 +1001000173.F9 LOW 1001000173.F9 +1001000173.G6 HIGH 1001000173.G6 +1001000173.A9 LOW 1001000173.A9 +1001000173.D2 HIGH 1001000173.D2 +1001000173.F2 LOW 1001000173.F2 +1001000173.H9 LOW 1001000173.H9 +1001000173.G1 LOW 1001000173.G1 +1001000173.B3 LOW 1001000173.B3 +1001000173.D7 HIGH 1001000173.D7 +1001000173.A12 LOW 1001000173.A12 +1001000173.C1 LOW 1001000173.C1 +1001000173.H7 HIGH 1001000173.H7 +1001000173.H5 LOW 1001000173.H5 +1001000173.G2 LOW 1001000173.G2 +1001000173.A3 LOW 1001000173.A3 +1001000173.D3 LOW 1001000173.D3 +1001000173.E1 LOW 1001000173.E1 +1001000173.G12 HIGH 1001000173.G12 +1001000173.C10 HIGH 1001000173.C10 +1001000173.C3 LOW 1001000173.C3 +1001000173.A5 LOW 1001000173.A5 +1001000173.G4 LOW 1001000173.G4 +1001000173.B11 LOW 1001000173.B11 +1001000173.G9 HIGH 1001000173.G9 +1001000173.F1 LOW 1001000173.F1 +1001000173.D8 LOW 1001000173.D8 +1001000173.E12 HIGH 1001000173.E12 +1001000173.F11 LOW 1001000173.F11 +1001000173.E5 LOW 1001000173.E5 +1001000173.G10 LOW 1001000173.G10 +1001000173.B9 LOW 1001000173.B9 +1001000173.C7 HIGH 1001000173.C7 +1001000173.B2 LOW 1001000173.B2 +1001000173.H4 LOW 1001000173.H4 +1001000174.G5 LOW 1001000174.G5 +1001000174.H9 LOW 1001000174.H9 +1001000174.A10 LOW 1001000174.A10 +1001000174.G10 HIGH 1001000174.G10 +1001000174.C8 LOW 1001000174.C8 +1001000174.F6 LOW 1001000174.F6 +1001000174.B4 LOW 1001000174.B4 +1001000174.H7 LOW 1001000174.H7 +1001000174.E10 HIGH 1001000174.E10 +1001000174.D5 LOW 1001000174.D5 +1001000174.E5 LOW 1001000174.E5 +1001000174.B11 LOW 1001000174.B11 +1001000174.F10 LOW 1001000174.F10 +1001000174.A5 LOW 1001000174.A5 +1001000174.B8 LOW 1001000174.B8 +1001000174.F2 LOW 1001000174.F2 +1001000174.F9 HIGH 1001000174.F9 +1001000174.F4 HIGH 1001000174.F4 +1001000174.B6 LOW 1001000174.B6 +1001000174.E2 LOW 1001000174.E2 +1001000174.G2 LOW 1001000174.G2 +1001000174.D8 LOW 1001000174.D8 +1001000174.H6 LOW 1001000174.H6 +1001000174.C3 HIGH 1001000174.C3 +1001000174.B7 LOW 1001000174.B7 +1001000174.A7 LOW 1001000174.A7 +1001000174.H10 LOW 1001000174.H10 +1001000174.F7 HIGH 1001000174.F7 +1001000174.A2 LOW 1001000174.A2 +1001000174.E4 LOW 1001000174.E4 +1001000174.D12 LOW 1001000174.D12 +1001000174.H4 LOW 1001000174.H4 +1001000174.C5 LOW 1001000174.C5 +1001000174.E9 LOW 1001000174.E9 +1001000174.D1 LOW 1001000174.D1 +1001000174.G4 LOW 1001000174.G4 +1001000174.G9 LOW 1001000174.G9 +1001000174.D4 HIGH 1001000174.D4 +1001000174.H11 HIGH 1001000174.H11 +1001000174.A9 LOW 1001000174.A9 +1001000174.A4 HIGH 1001000174.A4 +1001000174.C7 LOW 1001000174.C7 +1001000174.D11 LOW 1001000174.D11 +1001000174.F5 LOW 1001000174.F5 +1001000174.G6 LOW 1001000174.G6 +1001000174.D6 LOW 1001000174.D6 +1001000174.H3 LOW 1001000174.H3 +1001000174.F12 LOW 1001000174.F12 +1001000174.E6 LOW 1001000174.E6 +1001000174.G3 LOW 1001000174.G3 +1001000174.A8 LOW 1001000174.A8 |