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SaimMomin12
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Thanks @mirelaminkova 🚀
Some of the comments inline.
| @@ -1,18 +1,14 @@ | |||
| <tool id="odgi_build" name="odgi build" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> | |||
| <tool id="odgi_build" name="odgi build" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.1"> | |||
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| <tool id="odgi_build" name="odgi build" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.1"> | |
| <tool id="odgi_build" name="odgi build" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
We can introduce above TOKEN in macros.xml
| @@ -0,0 +1,76 @@ | |||
| <tool id="odgi_cover" name="odgi cover" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.1"> | |||
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| <tool id="odgi_cover" name="odgi cover" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.1"> | |
| <tool id="odgi_cover" name="odgi cover" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
| <inputs> | ||
| <expand macro="graph_input_param"/> | ||
| <param argument="--hogwild-depth" type="float" optional="true" min="0" label="Cover graph to this average depth" help="Randomly cover the graph until reaching the specified average depth."/> | ||
| <param argument="--num-paths-per-component" type="integer" optional="true" min="1" label="Number of paths to generate per component"/> |
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| <param argument="--num-paths-per-component" type="integer" optional="true" min="1" label="Number of paths to generate per component"/> | |
| <param argument="--num-paths-per-component" type="integer" optional="true" value="" min="1" label="Number of paths to generate per component"/> |
Please add value="" whereever the param is optional
| <param argument="--save-coverages" type="boolean" truevalue="true" falsevalue="" checked="false" label="Write node coverages table" help="Generate a tabular file with per-node coverage statistics."/> | ||
| </inputs> | ||
| <outputs> | ||
| <data name="output" format="odgi" label="${tool.name} on ${on_string}"/> |
| <param argument="--save-coverages" type="boolean" truevalue="true" falsevalue="" checked="false" label="Write node coverages table" help="Generate a tabular file with per-node coverage statistics."/> | ||
| </inputs> | ||
| <outputs> | ||
| <data name="output" format="odgi" label="${tool.name} on ${on_string}"/> |
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| <data name="output" format="odgi" label="${tool.name} on ${on_string}"/> | |
| <data name="output" format="odgi" label="${tool.name} on ${on_string}: Output graph"/> |
| @@ -0,0 +1,138 @@ | |||
| <tool id="odgi_layout" name="odgi layout" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.1"> | |||
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| <tool id="odgi_layout" name="odgi layout" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.1"> | |
| <tool id="odgi_layout" name="odgi layout" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
| <token name="@TOOL_VERSION@">0.3</token> | ||
| <token name="@VERSION_SUFFIX@">1</token> | ||
| <token name="@TOOL_VERSION@">0.9.3</token> | ||
| <token name="@VERSION_SUFFIX@">0</token> |
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| <token name="@VERSION_SUFFIX@">0</token> | |
| <token name="@VERSION_SUFFIX@">0</token> | |
| <token name="@PROFILE@">25.1</token> |
| @@ -0,0 +1,51 @@ | |||
| <tool id="odgi_normalize" name="odgi normalize" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.1"> | |||
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| <tool id="odgi_normalize" name="odgi normalize" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.1"> | |
| <tool id="odgi_normalize" name="odgi normalize" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
| @@ -0,0 +1,62 @@ | |||
| <tool id="odgi_overlap" name="odgi overlap" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.1"> | |||
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| <tool id="odgi_overlap" name="odgi overlap" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.1"> | |
| <tool id="odgi_overlap" name="odgi overlap" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
| @@ -0,0 +1,85 @@ | |||
| <tool id="odgi_paths" name="odgi paths" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.1"> | |||
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| <tool id="odgi_paths" name="odgi paths" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.1"> | |
| <tool id="odgi_paths" name="odgi paths" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
Please change this throughout
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Adding new odgi tools + fixing tests for some of the existing tools from #7371