Mercurial > repos > bgruening > nanopolish_eventalign
changeset 6:855b7ba0ce9c draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 4883f9a9a2779e2b4792314bd6128c7c109c00e1"
| author | bgruening |
|---|---|
| date | Fri, 07 May 2021 06:49:26 +0000 |
| parents | 8fdb079ddaf0 |
| children | 85a394edc247 |
| files | nanopolish_eventalign.xml test-data/all_fasta.loc test-data/all_fasta.loc.sample tool-data/all_fasta.loc.sample |
| diffstat | 4 files changed, 6 insertions(+), 22 deletions(-) [+] |
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--- a/nanopolish_eventalign.xml Fri May 29 13:29:43 2020 -0400 +++ b/nanopolish_eventalign.xml Fri May 07 06:49:26 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="nanopolish_eventalign" name="Nanopolish eventalign" version="@VERSION@+galaxy0"> +<tool id="nanopolish_eventalign" name="Nanopolish eventalign" version="@VERSION@+galaxy1"> <description>- Align nanopore events to reference k-mers</description> <macros> <import>macros.xml</import> @@ -49,6 +49,7 @@ --threads "\${GALAXY_SLOTS:-4}" $samples $scale_events + $signal_index $sam $print_read_names #if $w and str($w).strip(): @@ -110,6 +111,10 @@ label="Write the raw samples for the event to the tsv output" /> <param name="scale_events" argument="--scale-events" type="boolean" truevalue="--scale-events" falsevalue="" checked="false" label="Scale events to the model, rather than vice-versa" /> + <param name="signal_index" argument="--signal-index" type="boolean" truevalue="--signal-index" falsevalue="" checked="false" + label="write the raw signal start and end index values for the event to the tsv output" /> + + <param argument="--sam" type="boolean" truevalue="--sam" falsevalue="" checked="false" label="write output in SAM format" /> <param name="print_read_names" argument="--print-read-names" type="boolean" truevalue="--print-read-names" falsevalue="" checked="false"
--- a/test-data/all_fasta.loc Fri May 29 13:29:43 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -draft draft draft ${__HERE__}/draft.fa \ No newline at end of file
--- a/test-data/all_fasta.loc.sample Fri May 29 13:29:43 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -draft draft draft ${__HERE__}/draft.fa \ No newline at end of file
--- a/tool-data/all_fasta.loc.sample Fri May 29 13:29:43 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,19 +0,0 @@ -#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. -# -