| Previous changeset 11:563c3aa769f2 (2021-09-27) Next changeset 13:24d024316465 (2024-04-09) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iqtree/ commit 3b1c44e42b042ccbbe2d9e01c77d18f109d4984f" |
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modified:
iqtree.xml iqtree_macros.xml |
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| diff -r 563c3aa769f2 -r 9b892d7f82cc iqtree.xml --- a/iqtree.xml Mon Sep 27 15:55:35 2021 +0000 +++ b/iqtree.xml Sat Nov 27 09:45:09 2021 +0000 |
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| @@ -1,7 +1,6 @@ -<tool id="iqtree" name="IQ-TREE" version="@TOOL_VERSION@+@VERSION_SUFFIX@" > +<tool id="iqtree" name="IQ-TREE" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" > <description>Phylogenomic / evolutionary tree construction from multiple sequences</description> <macros> - <token name="@VERSION_SUFFIX@">galaxy2</token> <import>iqtree_macros.xml</import> </macros> <expand macro="requirements" /> @@ -23,7 +22,7 @@ #if $general_options.o -o '$general_options.o' #end if - +--seqtype $general_options.seqtype ## file #if $general_options.t -t '$general_options.t' @@ -545,22 +544,22 @@ </param> <when value="none" /> <when value="p"> - <param argument="-p" type="data" format="nex" optional="true" label="Partition file" /> + <param argument="-p" name="model_file" type="data" format="nex" optional="true" label="Partition file" /> <param argument="--subsample" type="integer" optional="true" label="Subsample partitions" help="Use a negative value for complement" /> <param argument="--subsample-seed" type="integer" optional="true" label="Subsampling random seed" help="Use a negative value for complement" /> </when> <when value="q"> - <param argument="-q" type="data" format="nex" optional="true" label="Partition file" /> + <param argument="-q" name="model_file" type="data" format="nex" optional="true" label="Partition file" /> <param argument="--subsample" type="integer" optional="true" label="Subsample partitions" help="Use a negative value for complement" /> <param argument="--subsample-seed" type="integer" optional="true" label="Subsampling random seed" help="Use a negative value for complement" /> </when> <when value="Q"> - <param argument="-Q" type="data" format="nex" optional="true" label="Partition file" /> + <param argument="-Q" name="model_file" type="data" format="nex" optional="true" label="Partition file" /> <param argument="--subsample" type="integer" optional="true" label="Subsample partitions" help="Use a negative value for complement" /> <param argument="--subsample-seed" type="integer" optional="true" label="Subsampling random seed" help="Use a negative value for complement" /> </when> <when value="S"> - <param argument="-S" type="data" format="nex" optional="true" label="Partition file" /> + <param argument="-S" name="model_file" type="data" format="nex" optional="true" label="Partition file" /> <param argument="--subsample" type="integer" optional="true" label="Subsample partitions" help="Use a negative value for complement" /> <param argument="--subsample-seed" type="integer" optional="true" label="Subsampling random seed" help="Use a negative value for complement" /> </when> @@ -705,7 +704,7 @@ <tests> <test expect_num_outputs="5"> <param name="seed" value="1257" /> - <param name="seqtype" value="AA" /> + <param name="seqtype" value="DNA" /> <param name="s" value="example.phy" /> <param name="m" value="TEST" /> <param name="msub" value="nuclear" /> @@ -751,7 +750,7 @@ <test expect_num_outputs="5"> <!-- bootstrap sans model --> <param name="seed" value="1257" /> - <param name="seqtype" value="AA" /> + <param name="seqtype" value="DNA" /> <param name="s" value="example.phy" /> <!-- <param name="m" value="TESTONLY" /> --> <param name="msub" value="nuclear" /> @@ -785,7 +784,7 @@ <test expect_num_outputs="5"> <!-- model sans bootstrap --> <param name="seed" value="1257" /> - <param name="seqtype" value="AA" /> + <param name="seqtype" value="DNA" /> <param name="s" value="example.phy" /> <param name="m" value="TESTONLY" /> <param name="msub" value="nuclear" /> |
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| diff -r 563c3aa769f2 -r 9b892d7f82cc iqtree_macros.xml --- a/iqtree_macros.xml Mon Sep 27 15:55:35 2021 +0000 +++ b/iqtree_macros.xml Sat Nov 27 09:45:09 2021 +0000 |
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| @@ -1,5 +1,6 @@ <macros> <token name="@TOOL_VERSION@">2.1.2</token> + <token name="@VERSION_SUFFIX@">2</token> <xml name="requirements"> <requirements> |