Mercurial > repos > iuc > stacks_refmap
changeset 12:d7a482f44e08 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 74ee33c6e30744a6da8deb7116d431d80ee80edb
| author | iuc |
|---|---|
| date | Fri, 07 Apr 2023 22:02:19 +0000 |
| parents | 1ba1185929c1 |
| children | |
| files | macros.xml stacks_refmap.xml |
| diffstat | 2 files changed, 12 insertions(+), 12 deletions(-) [+] |
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--- a/macros.xml Tue Mar 22 23:18:13 2022 +0000 +++ b/macros.xml Fri Apr 07 22:02:19 2023 +0000 @@ -343,7 +343,7 @@ <option value="fixed">Fixed</option> </param> <when value="snp"> - <param name="alpha" argument="--alpha" type="select" label="Chi square significance level required to call a heterozygote or homozygote" > + <param argument="--alpha" type="select" label="Chi square significance level required to call a heterozygote or homozygote" > <option value="0.1">0.1</option> <option value="0.05" selected="True">0.05</option> <option value="0.01">0.01</option> @@ -351,9 +351,9 @@ </param> </when> <when value="bounded"> - <param name="bound_low" argument="--bound_low" type="float" value="0.0" min="0.0" max="1.0" label="lower bound for epsilon, the error rate" help="between 0 and 1.0"/> - <param name="bound_high" argument="--bound_high" type="float" value="1.0" min="0.0" max="1.0" label="upper bound for epsilon, the error rate" help="between 0 and 1.0" /> - <param name="alpha" argument="--alpha" type="select" label="Chi square significance level required to call a heterozygote or homozygote" > + <param argument="--bound_low" type="float" value="0.0" min="0.0" max="1.0" label="lower bound for epsilon, the error rate" help="between 0 and 1.0"/> + <param argument="--bound_high" type="float" value="1.0" min="0.0" max="1.0" label="upper bound for epsilon, the error rate" help="between 0 and 1.0" /> + <param argument="--alpha" type="select" label="Chi square significance level required to call a heterozygote or homozygote" > <option value="0.1">0.1</option> <option value="0.05" selected="True">0.05</option> <option value="0.01">0.01</option> @@ -373,7 +373,7 @@ <option value="fixed">Fixed</option> </param> <when value="snp"> - <param name="alpha" argument="--alpha" type="select" label="Chi square significance level required to call a heterozygote or homozygote" > + <param argument="--alpha" type="select" label="Chi square significance level required to call a heterozygote or homozygote" > <option value="0.1">0.1</option> <option value="0.05" selected="True">0.05</option> <option value="0.01">0.01</option> @@ -381,9 +381,9 @@ </param> </when> <when value="bounded"> - <param name="bound_low" argument="--bound_low" type="float" value="0.0" min="0.0" max="1.0" label="lower bound for epsilon, the error rate" help="between 0 and 1.0"/> - <param name="bound_high" argument="--bound_high" type="float" value="1.0" min="0.0" max="1.0" label="upper bound for epsilon, the error rate" help="between 0 and 1.0" /> - <param name="alpha" argument="--alpha" type="select" label="Chi square significance level required to call a heterozygote or homozygote" > + <param argument="--bound_low" type="float" value="0.0" min="0.0" max="1.0" label="lower bound for epsilon, the error rate" help="between 0 and 1.0"/> + <param argument="--bound_high" type="float" value="1.0" min="0.0" max="1.0" label="upper bound for epsilon, the error rate" help="between 0 and 1.0" /> + <param argument="--alpha" type="select" label="Chi square significance level required to call a heterozygote or homozygote" > <option value="0.1">0.1</option> <option value="0.05" selected="True">0.05</option> <option value="0.01">0.01</option> @@ -391,7 +391,7 @@ </param> </when> <when value="fixed"> - <param name="bc_err_freq" argument="--bc_err_freq" type="float" value="0.1" min="0.0" max="1.0" label="Barcode error frequency" help="between 0 and 1.0"/> + <param argument="--bc_err_freq" type="float" value="0.1" min="0.0" max="1.0" label="Barcode error frequency" help="between 0 and 1.0"/> </when> </conditional> </xml>
--- a/stacks_refmap.xml Tue Mar 22 23:18:13 2022 +0000 +++ b/stacks_refmap.xml Fri Apr 07 22:02:19 2023 +0000 @@ -1,9 +1,9 @@ <tool id="stacks_refmap" name="Stacks: reference map" version="@WRAPPER_VERSION@.0"> <description>the Stacks pipeline with a reference genome (ref_map.pl)</description> - <expand macro="bio_tools"/> <macros> <import>macros.xml</import> </macros> + <expand macro="bio_tools"/> <expand macro="requirements"/> <expand macro="stdio"/> <command><![CDATA[ @@ -151,8 +151,8 @@ </when> </conditional> - <param name="m" type="integer" value="3" label="Minimum depth of coverage" help="specify the minimum depth of coverage to report a stack in pstacks" argument="-m" /> - <param name="P" type="integer" value="" optional="true" label="Minimum depth of coverage in 'progeny' individuals" help="specify the minimum depth of coverage to report a stack in pstacks for 'progeny' individuals" argument="-P" /> + <param argument="-m" type="integer" value="3" label="Minimum depth of coverage" help="specify the minimum depth of coverage to report a stack in pstacks" /> + <param argument="-P" type="integer" value="" optional="true" label="Minimum depth of coverage in 'progeny' individuals" help="specify the minimum depth of coverage to report a stack in pstacks for 'progeny' individuals" /> <!-- SNP Model options --> <section name="snp_options" title="SNP_Model_Options" expanded="False">