| Previous changeset 6:19c265784f35 (2021-11-27) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit ddb5e058a7877e627ed24ef8cb9a046ccb450cb4 |
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modified:
lastal.xml lastdb.xml lastsplit.xml lasttrain.xml macros_last.xml maf-convert.xml |
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| diff -r 19c265784f35 -r eca7ac1eb423 lastal.xml --- a/lastal.xml Sat Nov 27 10:12:45 2021 +0000 +++ b/lastal.xml Mon Oct 23 20:45:02 2023 +0000 |
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| @@ -1,15 +1,10 @@ -<tool id="last_al" name="LASTal" version="@TOOL_VERSION@+galaxy1" profile="20.01"> - +<tool id="last_al" name="LASTal" version="@TOOL_VERSION@+galaxy2" profile="20.01"> <description>finds local alignments between query sequences, and reference sequences.</description> - <expand macro="bio_tools"/> <macros> <import>macros_last.xml</import> </macros> - - <requirements> - <requirement type="package" version="@TOOL_VERSION@">last</requirement> - </requirements> - + <expand macro="bio_tools"/> + <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ set -e -o pipefail; |
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| diff -r 19c265784f35 -r eca7ac1eb423 lastdb.xml --- a/lastdb.xml Sat Nov 27 10:12:45 2021 +0000 +++ b/lastdb.xml Mon Oct 23 20:45:02 2023 +0000 |
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| @@ -1,15 +1,10 @@ -<tool id="last_db" name="LASTdb" version="@TOOL_VERSION@+galaxy0" profile="20.01"> - +<tool id="last_db" name="LASTdb" version="@TOOL_VERSION@+galaxy1" profile="20.01"> <description>prepares sequences for subsequent comparison and alignment using lastal.</description> - <expand macro="bio_tools"/> <macros> <import>macros_last.xml</import> </macros> - - <requirements> - <requirement type="package" version="@TOOL_VERSION@">last</requirement> - </requirements> - + <expand macro="bio_tools"/> + <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ set -e -o pipefail; @@ -140,9 +135,7 @@ </inputs> <outputs> - <data name="outfile" format="lastdb"> - <discover_datasets pattern="__designation__" directory="ref_genome"/> - </data> + <data name="outfile" format="lastdb"/> </outputs> <tests> |
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| diff -r 19c265784f35 -r eca7ac1eb423 lastsplit.xml --- a/lastsplit.xml Sat Nov 27 10:12:45 2021 +0000 +++ b/lastsplit.xml Mon Oct 23 20:45:02 2023 +0000 |
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| @@ -1,15 +1,10 @@ -<tool id="last_split" name="LAST-split" version="@TOOL_VERSION@+galaxy0" profile="20.01"> - +<tool id="last_split" name="LAST-split" version="@TOOL_VERSION@+galaxy1" profile="20.01"> <description>finds "split alignments" (typically for DNA) or "spliced alignments" (typically for RNA).</description> - <expand macro="bio_tools"/> <macros> <import>macros_last.xml</import> </macros> - - <requirements> - <requirement type="package" version="@TOOL_VERSION@">last</requirement> - </requirements> - + <expand macro="bio_tools"/> + <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ #if $db_opts.db_opts_input == 'lastdb' ln -s '$db_opts.lastdatabase.extra_files_path' './db_files' && |
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| diff -r 19c265784f35 -r eca7ac1eb423 lasttrain.xml --- a/lasttrain.xml Sat Nov 27 10:12:45 2021 +0000 +++ b/lasttrain.xml Mon Oct 23 20:45:02 2023 +0000 |
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| @@ -1,15 +1,10 @@ -<tool id="last_train" name="LAST-train" version="@TOOL_VERSION@+galaxy0" profile="20.01"> - +<tool id="last_train" name="LAST-train" version="@TOOL_VERSION@+galaxy1" profile="20.01"> <description>finds the rates (probabilities) of insertion, deletion, and substitutions between two sets of sequences.</description> - <expand macro="bio_tools"/> <macros> <import>macros_last.xml</import> </macros> - - <requirements> - <requirement type="package" version="@TOOL_VERSION@">last</requirement> - </requirements> - + <expand macro="bio_tools"/> + <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ set -e -o pipefail; #if $db_opts.db_opts_input == 'lastdb' |
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| diff -r 19c265784f35 -r eca7ac1eb423 macros_last.xml --- a/macros_last.xml Sat Nov 27 10:12:45 2021 +0000 +++ b/macros_last.xml Mon Oct 23 20:45:02 2023 +0000 |
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| @@ -1,7 +1,7 @@ <macros> <token name="@TOOL_VERSION@">1205</token> <token name="@LAST_HELP@"><![CDATA[ - Documentation : http://last.cbrc.jp/ + Documentation : https://gitlab.com/mcfrith/last LAST finds similar regions between sequences. @@ -20,6 +20,11 @@ - Train alignment parameters for unusual kinds of sequence (e.g. nanopore). ]]></token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">last</requirement> + </requirements> + </xml> <xml name="bio_tools"> <xrefs> <xref type="bio.tools">last</xref> @@ -36,7 +41,7 @@ <option value="lastdb" selected="true">LAST database from history</option> </param> <when value="db"> - <param name="database" type="select" multiple="true" label="LAST database"> + <param name="database" type="select" label="LAST database"> <options from_data_table="lastdb" /> </param> </when> |
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| diff -r 19c265784f35 -r eca7ac1eb423 maf-convert.xml --- a/maf-convert.xml Sat Nov 27 10:12:45 2021 +0000 +++ b/maf-convert.xml Mon Oct 23 20:45:02 2023 +0000 |
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| @@ -1,15 +1,10 @@ -<tool id="last_maf_convert" name="MAF-convert" version="@TOOL_VERSION@+galaxy0" profile="20.01"> - +<tool id="last_maf_convert" name="MAF-convert" version="@TOOL_VERSION@+galaxy1" profile="20.01"> <description>read MAF-format alignments and write them in another format.</description> - <expand macro="bio_tools"/> <macros> <import>macros_last.xml</import> </macros> - - <requirements> - <requirement type="package" version="@TOOL_VERSION@">last</requirement> - </requirements> - + <expand macro="bio_tools"/> + <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ maf-convert |