Mercurial > repos > iuc > fastk_fastk
diff fastk.xml @ 0:ff827f983bbb draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastk commit 57fa4dcee2aaa115df4a5b7173a3a8fb889bc5a3
| author | iuc |
|---|---|
| date | Fri, 03 May 2024 20:23:04 +0000 |
| parents | |
| children | b820ef95ca20 |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fastk.xml Fri May 03 20:23:04 2024 +0000 @@ -0,0 +1,114 @@ +<tool id="fastk_fastk" name="FastK" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.2"> + <description>A k-mer counter for high-quality assembly datasets</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ + mkdir -p outfiles/tmpfiles && + #if $infile.is_of_type("fastq"): + #set INPUTFILE="input.fastq" + #elif $infile.is_of_type("fastq.gz"): + #set INPUTFILE="input.fastq.gz" + #else + #set INPUTFILE="input."+$infile.ext + #end if + ln -s '$infile' $INPUTFILE && + FastK $INPUTFILE + -k$kmer_size + #if $sorted_table.sorted_table_option == 'yes_with_default': + -t + #elif $sorted_table.sorted_table_option == 'yes_with_custom': + -t$sorted_table_cutoff + #end if + -T\${GALAXY_SLOTS:-8} -Noutfiles/output -Poutfiles/tmpfiles + #if $sorted_table.sorted_table_option == 'yes_with_default': + && Tabex outfiles/output.ktab -t${sorted_table.tabex_threshold_for_default} LIST > '$tabex_hist' + #elif $sorted_table.sorted_table_option == 'yes_with_custom': + && Tabex outfiles/output.ktab -t${sorted_table.tabex_threshold_for_custom} LIST > '$tabex_hist' + #end if + && tar -c -f fastk.tar ./outfiles/ + ]]></command> + <inputs> + <param name="infile" type="data" format="fasta,fasta.gz,fastq,fastq.gz,cram,unsorted.bam,sam" label="Input file"/> + <param name="kmer_size" argument="-k" type="integer" min="5" max="50" value="40" label="Enter desired k-mer size" help="Default: 40" /> + <conditional name="sorted_table"> + <param name="sorted_table_option" type="select" label="Sort table" help="Do you want a sorted table of all canonical k-mers and their counts? The sorted table is sorted lexicographically on the k-mer where a < c < g < t."> + <option value="no">No</option> + <option value="yes_with_default">Yes, Default sorted </option> + <option value="yes_with_custom">Yes, Custom sorted </option> + </param> + <when value="no"/> + <when value="yes_with_default"> + <param name="tabex_threshold_for_default" argument="-t" type="integer" value="5" min="1" label="Tabex count threshold" help="Trim all k-mers with counts less than threshold"/> + </when> + <when value="yes_with_custom"> + <param name="sorted_table_cutoff" type="integer" min="2" value="10" label="Enter sorted table cutoff value"/> + <param name="tabex_threshold_for_custom" argument="-t" type="integer" value="5" min="1" label="Tabex count threshold" help="Trim all k-mers with counts less than threshold"/> + </when> + </conditional> + </inputs> + <outputs> + <data name="fastk_out" format="tar" from_work_dir="fastk.tar" label="${tool.name} on ${on_string}: FastK files"/> + <data name="fastk_hist_out" format="fastk_hist" from_work_dir="outfiles/output.hist" label="${tool.name} on ${on_string}: FastK hist" /> + <data name="tabex_hist" format="txt" label="${tool.name} on ${on_string}: Tabex output"> + <filter> sorted_table['sorted_table_option'] != 'no' </filter> + </data> + </outputs> + <tests> + <!-- TEST 1 --> + <test expect_num_outputs="2"> + <param name="infile" value="input01.fasta.gz"/> + <output name="fastk_out" ftype="tar"> + <assert_contents> + <has_archive_member path="./outfiles/output.hist"/> + </assert_contents> + </output> + </test> + <!-- TEST 2 --> + <test expect_num_outputs="3"> + <param name="infile" value="input01.fasta.gz"/> + <conditional name="sorted_table"> + <param name="sorted_table_option" value="yes_with_default"/> + </conditional> + <output name="fastk_out" ftype="tar"> + <assert_contents> + <has_archive_member path="./outfiles/output.hist"/> + <has_archive_member path="./outfiles/output.ktab"/> + </assert_contents> + </output> + <output name="tabex_hist" value="test02.tabex.txt"/> + </test> + <!-- TEST 3 --> + <test expect_num_outputs="3"> + <param name="infile" value="input01.fasta.gz"/> + <conditional name="sorted_table"> + <param name="sorted_table_option" value="yes_with_custom"/> + <param name="sorted_table_cutoff" value="5"/> + </conditional> + <output name="fastk_out" ftype="tar"> + <assert_contents> + <has_archive_member path="./outfiles/output.hist"/> + <has_archive_member path="./outfiles/output.ktab"/> + </assert_contents> + </output> + <output name="tabex_hist" value="test03.tabex.txt"/> + </test> + </tests> + <help><![CDATA[ + FastK is a k‑mer counter that is optimized for processing high quality DNA assembly data sets such as those produced with an Illumina instrument or a PacBio run in HiFi mode. + + The input data can be in CRAM, BAM, SAM, fasta, or fastq files. + + FastK produces the following outputs: + + 1. FastK hist: file in binary format containing histogram information detailing the frequency of occurrence for each k‑mer within the dataset. + + 2. A Tabex txt file comprising a table of k‑mer/count pairs, sorted lexicographically on the k‑mer sequence, followingthe order a < c < g < t + + 3. A tar file comprising of hidden .ktab files that can be used for downstream FASTK tools. + + + ]]></help> + <expand macro="citations"/> +</tool> \ No newline at end of file