| Next changeset 1:ebe4463404b4 (2019-05-15) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bandage commit d5e71a9c6eeb449a00c335a244e5348c9bd49c16 |
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added:
bandage_image.xml bandage_info.xml macros.xml static/images/bandage_graph.png test-data/gfa.tabular test-data/out.jpg test-data/out.png test-data/out.svg test-data/out.txt test-data/out_standard.txt |
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| diff -r 000000000000 -r 067592b6b312 bandage_image.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bandage_image.xml Tue Sep 18 05:41:44 2018 -0400 |
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| @@ -0,0 +1,70 @@ +<tool id="bandage_image" name="Bandage Image" version="@TOOL_VERSION@+galaxy0"> + <description>visualize de novo assembly graphs</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="version_command"/> + <command detect_errors="exit_code"> + <![CDATA[ +Bandage + image + '$input_file' + 'out.$output_format' + #if $height: + --height '$height' + #end if + #if $width: + --width '$width' + #end if + ]]></command> + <inputs> + <param name="input_file" type="data" format="tabular" label="Graphical Fragment Assembly" /> + <param argument="--height" type="integer" min="1" value="1000" optional="True" label="Image height" help="If only height or width is set, the other will be determined automatically. If both are set, the image will be exactly that size. Default: 1000."/> + <param argument="--width" type="integer" min="1" optional="True" label="Image width" help="If only height or width is set, the other will be determined automatically. If both are set, the image will be exactly that size. Default: not set."/> + <param name="output_format" type="select" label="Produce jpg, png or svg file?"> + <option selected="True" value="jpg">.jpg</option> + <option value="png">.png</option> + <option value="svg">.svg</option> + </param> + </inputs> + <outputs> + <data name="outfile" format="jpg" from_work_dir="out.*" label="${tool.name} on ${on_string}: Assembly Graph Image"> + <change_format> + <when input="output_format" value="png" format="png"/> + <when input="output_format" value="svg" format="svg"/> + </change_format> + </data> + </outputs> + <tests> + <test> + <param name="input_file" ftype="tabular" value="gfa.tabular"/> + <output name="outfile" ftype="jpg" file="out.jpg" compare="sim_size" delta="70000"/> + </test> + <test> + <param name="input_file" ftype="tabular" value="gfa.tabular"/> + <param name="height" value="100"/> + <param name="width" value="100"/> + <param name="output_format" value="png"/> + <output name="outfile" ftype="png" file="out.png" compare="sim_size" delta="120000"/> + </test> + <test> + <param name="input_file" ftype="tabular" value="gfa.tabular"/> + <param name="output_format" value="svg"/> + <output name="outfile" ftype="svg" file="out.svg" compare="sim_size" delta="120000"/> + </test> + </tests> + <help><![CDATA[ +@BANDAGE_OVERVIEW@ + +**Command Documentation** + +``Bandage image`` will generate an image file of the graph visualisation. + +.. image:: $PATH_TO_IMAGES/bandage_graph.png + :alt: example bandage plot + + ]]></help> + <expand macro="citations"/> +</tool> + |
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| diff -r 000000000000 -r 067592b6b312 bandage_info.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bandage_info.xml Tue Sep 18 05:41:44 2018 -0400 |
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| @@ -0,0 +1,77 @@ +<tool id="bandage_info" name="Bandage Info" version="@TOOL_VERSION@+galaxy0"> + <description>determine statistics of de novo assembly graphs</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="version_command"/> + <command detect_errors="exit_code"> + <![CDATA[ +Bandage + info + '$input_file' + $tsv + > out.txt + ]]></command> + <inputs> + <param name="input_file" type="data" format="tabular" label="Graphical Fragment Assembly" /> + <param argument="--tsv" type="boolean" checked="false" truevalue="--tsv" falsevalue="" label="Output the information in a single tab-delimited line starting with the graph file"/> + </inputs> + <outputs> + <data name="outfile" format="txt" from_work_dir="out.txt" label="${tool.name} on ${on_string}: Assembly Graph Information"/> + </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"/> + </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"/> + </test> + </tests> + <help><![CDATA[ + +@BANDAGE_OVERVIEW@ + +**Command Documentation** + +``Bandage info`` takes a graph file as input and outputs the following statistics about the graph: + +- **Node count:** The number of nodes in the graph. Only positive nodes are counted (i.e. each complementary pair counts as one). +- **Edge count:** The number of edges in the graph. Only one edge in each complementary pair is counted. +- **Total length:** The total number of base pairs in the graph. +- **Dead ends:** The number of instances where an end of a node does not connect to any other nodes. +- **Percentage dead ends:** The proportion of possible dead ends. The maximum number of dead ends is twice the number of nodes (occurs when there are no edges), so this value is the number of dead ends divided by twice the node count. +- **Connected components:** The number of regions of the graph which are disconnected from each other. +- **Largest component:** The total number of base pairs in the largest connected component. +- **N50:** Nodes that are this length or greater will collectively add up to at least half of the total length. +- **Shortest node:** The length of the shortest node in the graph. +- **Lower quartile node:** The median node length for the shorter half of the nodes. +- **Median node:** The median node length for the graph. +- **Upper quartile node:** The median node length for the longer half of the nodes. +- **Longest node:** The length of the longest node in the graph. + +Example output:: + + Node count: 561 + Edge count: 734 + Total length (bp): 4878380 + Dead ends: 33 + Percentage dead ends: 2.94118% + Connected components: 19 + Largest component (bp): 4821329 + N50 (bp): 90360 + Shortest node (bp): 1 + Lower quartile node (bp): 17 + Median node (bp): 87 + Upper quartile node (bp): 404 + Longest node (bp): 205425 + + ]]></help> + <expand macro="citations"/> +</tool> + |
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| diff -r 000000000000 -r 067592b6b312 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Sep 18 05:41:44 2018 -0400 |
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| @@ -0,0 +1,27 @@ +<macros> + <token name="@TOOL_VERSION@">0.8.1</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">bandage</requirement> + </requirements> + </xml> + <xml name="version_command"> + <version_command>Bandage --version</version_command> + </xml> + <token name="@BANDAGE_OVERVIEW@"> + +**Bandage Overview** + +Bandage is a GUI program that allows users to interact with the assembly graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and others. +De novo assembly graphs contain not only assembled contigs but also the connections between those contigs, which were previously not easily accessible. Bandage visualises assembly graphs, with connections, using graph layout algorithms. Nodes in the drawn graph, which represent contigs, can be automatically labelled with their ID, length or depth. Users can interact with the graph by moving, labelling and colouring nodes. Sequence information can also be extracted directly from the graph viewer. By displaying connections between contigs, Bandage opens up new possibilities for analysing and improving de novo assemblies that are not possible by looking at contigs alone. + +Bandage works with Graphical Fragment Assembly (GFA) files. For more information about this file format, see here_ + +.. _here: https://gfa-spec.github.io/GFA-spec/GFA2.html + </token> + <xml name="citations"> + <citations> + <citation type="doi">10.1093/bioinformatics/btv383</citation> + </citations> + </xml> +</macros> |
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| diff -r 000000000000 -r 067592b6b312 static/images/bandage_graph.png |
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| diff -r 000000000000 -r 067592b6b312 test-data/gfa.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gfa.tabular Tue Sep 18 05:41:44 2018 -0400 |
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| b |
| diff -r 000000000000 -r 067592b6b312 test-data/out.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.txt Tue Sep 18 05:41:44 2018 -0400 |
| b |
| @@ -0,0 +1,2 @@ +455 1061 3348 4532 2238438 268863 12 1.31868% 7 1960789 277649 4421 736 4290 4404 4460 147170 1 +297647 |
| b |
| diff -r 000000000000 -r 067592b6b312 test-data/out_standard.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out_standard.txt Tue Sep 18 05:41:44 2018 -0400 |
| b |
| @@ -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 |
