| Previous changeset 4:94fe43e75ddc (2021-01-19) Next changeset 6:b9e31c5c01c7 (2021-11-27) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit 7823462e83ff5efbcfd3161f7d471fd07da51611" |
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modified:
bandage_image.xml bandage_info.xml macros.xml |
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added:
test-data/out.tab test-data/out_standard.tab |
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removed:
test-data/out.txt test-data/out_standard.txt |
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| diff -r 94fe43e75ddc -r d8b1027d6ce0 bandage_image.xml --- a/bandage_image.xml Tue Jan 19 10:06:26 2021 +0000 +++ b/bandage_image.xml Sun Sep 12 08:13:13 2021 +0000 |
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| @@ -1,5 +1,6 @@ <tool id="bandage_image" name="Bandage Image" version="@TOOL_VERSION@+galaxy3" profile="18.01"> <description>visualize de novo assembly graphs</description> + <expand macro="bio_tools"/> <macros> <import>macros.xml</import> </macros> |
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| diff -r 94fe43e75ddc -r d8b1027d6ce0 bandage_info.xml --- a/bandage_info.xml Tue Jan 19 10:06:26 2021 +0000 +++ b/bandage_info.xml Sun Sep 12 08:13:13 2021 +0000 |
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| @@ -1,5 +1,6 @@ -<tool id="bandage_info" name="Bandage Info" version="@TOOL_VERSION@+galaxy1" profile="18.01"> +<tool id="bandage_info" name="Bandage Info" version="@TOOL_VERSION@+galaxy2" profile="18.01"> <description>determine statistics of de novo assembly graphs</description> + <expand macro="bio_tools"/> <macros> <import>macros.xml</import> </macros> @@ -12,26 +13,27 @@ info '$input_file' $tsv - > out.txt + | sed 's/:\s\+/:\t/g' + > out.tab ]]></command> <inputs> <param name="input_file" type="data" format="txt" label="Graphical Fragment Assembly" help="Supports multiple assembly graph formats: LastGraph (Velvet), FASTG (SPAdes), Trinity.fasta, ASQG and GFA."/> <param argument="--tsv" type="boolean" checked="false" truevalue="--tsv" falsevalue="" label="Output the information in a single tab-delimited line starting with the graph file"/> </inputs> <outputs> - <data name="outfile" format="txt" from_work_dir="out.txt" label="${tool.name} on ${on_string}: Assembly Graph Information"/> + <data name="outfile" format="tabular" from_work_dir="out.tab" label="${tool.name} on ${on_string}: Assembly Graph Information"/> </outputs> <tests> <test> <param name="input_file" ftype="tabular" value="gfa.tabular"/> <param name="select_mode" value="info"/> <param name="tsv" value="True"/> - <output name="outfile" ftype="txt" file="out.txt" compare="contains"/> + <output name="outfile" ftype="tabular" file="out.tab" compare="contains"/> </test> <test> <param name="input_file" ftype="tabular" value="gfa.tabular"/> <param name="select_mode" value="info"/> - <output name="outfile" ftype="txt" file="out_standard.txt"/> + <output name="outfile" ftype="tabular" file="out_standard.tab"/> </test> </tests> <help><![CDATA[ @@ -65,7 +67,7 @@ Percentage dead ends: 2.94118% Connected components: 19 Largest component (bp): 4821329 - N50 (bp): 90360 + N50 (bp): 90360 Shortest node (bp): 1 Lower quartile node (bp): 17 Median node (bp): 87 @@ -75,4 +77,3 @@ ]]></help> <expand macro="citations"/> </tool> - |
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| diff -r 94fe43e75ddc -r d8b1027d6ce0 macros.xml --- a/macros.xml Tue Jan 19 10:06:26 2021 +0000 +++ b/macros.xml Sun Sep 12 08:13:13 2021 +0000 |
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| @@ -8,8 +8,12 @@ <xml name="version_command"> <version_command>@HEADLESS@ Bandage --version</version_command> </xml> - <token name="@HEADLESS@"><![CDATA[export QT_QPA_PLATFORM='offscreen' &&]]> -</token> + <xml name="bio_tools"> + <xrefs> + <xref type="bio.tools">bandage</xref> + </xrefs> + </xml> + <token name="@HEADLESS@"><![CDATA[export QT_QPA_PLATFORM='offscreen' &&]]></token> <token name="@BANDAGE_OVERVIEW@"> **Bandage Overview** |
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| diff -r 94fe43e75ddc -r d8b1027d6ce0 test-data/out.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.tab Sun Sep 12 08:13:13 2021 +0000 |
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| @@ -0,0 +1,2 @@ +455 1061 3348 4532 2238438 268863 12 1.31868% 7 1960789 277649 4421 736 4290 4404 4460 147170 1 +297647 |
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| diff -r 94fe43e75ddc -r d8b1027d6ce0 test-data/out.txt --- a/test-data/out.txt Tue Jan 19 10:06:26 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,2 +0,0 @@ -455 1061 3348 4532 2238438 268863 12 1.31868% 7 1960789 277649 4421 736 4290 4404 4460 147170 1 -297647 |
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| diff -r 94fe43e75ddc -r d8b1027d6ce0 test-data/out_standard.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out_standard.tab Sun Sep 12 08:13:13 2021 +0000 |
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| @@ -0,0 +1,19 @@ +Node count: 455 +Edge count: 1061 +Smallest edge overlap (bp): 3348 +Largest edge overlap (bp): 4532 +Total length (bp): 2238438 +Total length no overlaps (bp): 268863 +Dead ends: 12 +Percentage dead ends: 1.31868% +Connected components: 7 +Largest component (bp): 1960789 +Total length orphaned nodes (bp): 1960789 +N50 (bp): 4421 +Shortest node (bp): 736 +Lower quartile node (bp): 4290 +Median node (bp): 4404 +Upper quartile node (bp): 4460 +Longest node (bp): 147170 +Median depth: 1 +Estimated sequence length (bp): 297647 |
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| diff -r 94fe43e75ddc -r d8b1027d6ce0 test-data/out_standard.txt --- a/test-data/out_standard.txt Tue Jan 19 10:06:26 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,19 +0,0 @@ -Node count: 455 -Edge count: 1061 -Smallest edge overlap (bp): 3348 -Largest edge overlap (bp): 4532 -Total length (bp): 2238438 -Total length no overlaps (bp): 268863 -Dead ends: 12 -Percentage dead ends: 1.31868% -Connected components: 7 -Largest component (bp): 1960789 -Total length orphaned nodes (bp): 1960789 -N50 (bp): 4421 -Shortest node (bp): 736 -Lower quartile node (bp): 4290 -Median node (bp): 4404 -Upper quartile node (bp): 4460 -Longest node (bp): 147170 -Median depth: 1 -Estimated sequence length (bp): 297647 |