Mercurial > repos > bgruening > nanopolish_methylation
changeset 6:3b7b887676b2 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 25c22b467760e4784e199125292927bd2274a189
| author | bgruening |
|---|---|
| date | Sun, 23 Jun 2019 04:41:21 -0400 |
| parents | acd66f133ab3 |
| children | e94ca8d80a60 |
| files | nanopolish_methylation.xml test-data/all_fasta.loc test-data/all_fasta.loc.sample test-data/all_fasta.loc.test tool-data/all_fasta.loc.sample |
| diffstat | 5 files changed, 5 insertions(+), 25 deletions(-) [+] |
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--- a/nanopolish_methylation.xml Tue Jun 18 12:32:58 2019 -0400 +++ b/nanopolish_methylation.xml Sun Jun 23 04:41:21 2019 -0400 @@ -1,4 +1,4 @@ -<tool id="nanopolish_methylation" name="Nanopolish methylation" version="0.1.0"> +<tool id="nanopolish_methylation" name="Nanopolish methylation" version="0.11.1"> <description>- Classify nucleotides as methylated or not.</description> <macros> <import>macros.xml</import> @@ -55,7 +55,7 @@ <inputs> <!-- index inputs --> <param type="data" name="input_merged" format="fasta,fastq" label="Basecalled merged reads.fa"/> - <param type="data" name="input_reads_raw" format="h5,fast5.tar.gz,fast5.tar.bz2,fast5.tar" label="Flat archive file of raw fast5 files"/> + <param type="data" name="input_reads_raw" format="fast5.tar.gz,fast5.tar.bz2,fast5.tar" label="Flat archive file of raw fast5 files"/> <!-- variants consensus inputs --> <param type="data" argument="-b" format="bam" label="Reads aligned to the reference genome" /> @@ -105,8 +105,8 @@ <test> <param name="input_merged" ftype="fasta" value="reads.fasta" /> <param name="input_reads_raw" ftype="fast5.tar.gz" value="fast5_files.tar.gz" /> - <param name="reference_source_selector" value="cached" /> - <param name="ref_file" value="draft"/> + <param name="reference_source_selector" value="history" /> + <param name="ref_file" value="draft.fa"/> <param name="b" value="reads.sorted.bam" /> <param name="w" value="tig00000001:200000-202000" /> <param name="batchsize" value="512" />
--- a/test-data/all_fasta.loc Tue Jun 18 12:32:58 2019 -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 Tue Jun 18 12:32:58 2019 -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/all_fasta.loc.test Sun Jun 23 04:41:21 2019 -0400 @@ -0,0 +1,1 @@ +draft draft draft ${__HERE__}/draft.fa \ No newline at end of file
--- a/tool-data/all_fasta.loc.sample Tue Jun 18 12:32:58 2019 -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. -# -