Mercurial > repos > iuc > arriba
changeset 5:01ccd366690d draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 3a528b3f87cff585baf4abb8ebe0be95a24044ea
| author | iuc |
|---|---|
| date | Wed, 25 Oct 2023 08:24:37 +0000 |
| parents | 3d61a698e5e1 |
| children | |
| files | arriba.xml macros.xml test-data/all_fasta.loc test-data/genome.fasta.gz test-data/genome.fasta.gz.fai test-data/genome.fasta.gz.gzi tool_data_table_conf.xml.test |
| diffstat | 7 files changed, 33 insertions(+), 5 deletions(-) [+] |
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--- a/arriba.xml Fri Mar 24 08:12:45 2023 +0000 +++ b/arriba.xml Wed Oct 25 08:24:37 2023 +0000 @@ -472,8 +472,8 @@ <test expect_num_outputs="4"> <param name="input" ftype="sam" value="Aligned.out.sam"/> <conditional name="genome"> - <param name="genome_source" value="history"/> - <param name="assembly" ftype="fasta" value="genome.fasta.gz"/> + <param name="genome_source" value="cached"/> + <param name="ref_file" value="genome_id"/> </conditional> <conditional name="genome_gtf"> <param name="gtf_source" value="history"/>
--- a/macros.xml Fri Mar 24 08:12:45 2023 +0000 +++ b/macros.xml Wed Oct 25 08:24:37 2023 +0000 @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">2.4.0</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">arriba</requirement> @@ -53,7 +53,7 @@ ln -sf '$genome.assembly' $genome_assembly && #end if #elif str($genome.genome_source) == "cached" - #set $genome_assembly = $genome.ref_file.fields.fasta + #set $genome_assembly = $genome.ref_file.fields.path #end if ]]></token> <token name="@GTF_SOURCE@"><![CDATA[ @@ -63,7 +63,7 @@ ]]></token> <xml name="visualization_options"> - <param name="cytobands" argument="--cytobands" type="data" format="tabular" optional="true" label="Cytobands"/> + <param argument="--cytobands" type="data" format="tabular" optional="true" label="Cytobands"/> <section name="options" expanded="false" title="Draw Fusion Options"> <param argument="--sampleName" type="text" value="" optional="true" label="Sample Name printed as the title on every page"/> <param argument="--transcriptSelection" type="select" optional="true" label="Transcript selection">
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/all_fasta.loc Wed Oct 25 08:24:37 2023 +0000 @@ -0,0 +1,19 @@ +#This file lists the locations and dbkeys of all the fasta files +#under the "genome" directory (a directory that contains a directory +#for each build). The script extract_fasta.py will generate the file +#all_fasta.loc. This file has the format (white space characters are +#TAB characters): +# +#<unique_build_id> <dbkey> <display_name> <file_path> +# +#So, all_fasta.loc could look something like this: +# +#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa +# +#Your all_fasta.loc file should contain an entry for each individual +#fasta file. So there will be multiple fasta files for each build, +#such as with hg19 above. +# +genome_id dbkey genome_name ${__HERE__}/genome.fasta.gz \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genome.fasta.gz.fai Wed Oct 25 08:24:37 2023 +0000 @@ -0,0 +1,2 @@ +22 269079 4 269079 269080 +9 515509 269087 515509 515510
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Wed Oct 25 08:24:37 2023 +0000 @@ -0,0 +1,7 @@ +<tables> + <!-- Locations of all fasta files under genome directory --> + <table name="all_fasta" comment_char="#" allow_duplicate_entries="False"> + <columns>value, dbkey, name, path</columns> + <file path="${__HERE__}/test-data/all_fasta.loc" /> + </table> +</tables>