Mercurial > repos > iuc > last
changeset 10:a07c62dc88f9 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 88d7f81768f05f490f444b646f47241cf2547b44"
| author | iuc |
|---|---|
| date | Sat, 27 Nov 2021 10:11:58 +0000 |
| parents | 18ff8319181f |
| children | |
| files | lastal.xml lastal.xml.orig lastdb.xml lastdb.xml.orig lastsplit.xml lasttrain.xml macros_last.xml maf-convert.xml maf-convert.xml.orig |
| diffstat | 9 files changed, 12 insertions(+), 771 deletions(-) [+] |
line wrap: on
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--- a/lastal.xml Tue Aug 31 09:15:05 2021 +0000 +++ b/lastal.xml Sat Nov 27 10:11:58 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="last_al" name="LASTal" version="@LAST_CONDA_VERSION@+galaxy0" profile="20.01"> +<tool id="last_al" name="LASTal" version="@TOOL_VERSION@+galaxy1" profile="20.01"> <description>finds local alignments between query sequences, and reference sequences.</description> <expand macro="bio_tools"/> @@ -7,7 +7,7 @@ </macros> <requirements> - <requirement type="package" version="@LAST_CONDA_VERSION@">last</requirement> + <requirement type="package" version="@TOOL_VERSION@">last</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ @@ -77,6 +77,7 @@ -w $lastal.misc_opt.w -u $lastal.misc_opt.u -g $lastal.misc_opt.g + -G $lastal.misc_opt.G -P \${GALAXY_SLOTS:-1}
--- a/lastal.xml.orig Tue Aug 31 09:15:05 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,389 +0,0 @@ -<<<<<<< HEAD -<tool id="last_al" name="LASTal" version="@LAST_CONDA_VERSION@+galaxy0" profile="20.01"> - -======= -<tool id="last_al" name="LASTal" version="@LAST_CONDA_VERSION@+galaxy1" profile="18.01"> ->>>>>>> c37d72558 (add more bio.tool IDs) - <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="@LAST_CONDA_VERSION@">last</requirement> - </requirements> - <command detect_errors="exit_code"><![CDATA[ - set -e -o pipefail; - - #if $db_opts.db_opts_input == 'lastdb' - ln -s '$db_opts.lastdatabase.extra_files_path' './db_files' && - #end if - - #if $query_seq.ext.endswith('.gz') - zcat - #else - cat - #end if - '$query_seq' | lastal - - #if $query_seq.ext.startswith('fasta') - -Q 0 - #else if $query_seq.ext.startswith('fastqsanger') - -Q 1 - #else if $query_seq.ext.startswith('fastqsolexa') - -Q 2 - #else if $query_seq.ext.startswith('fastqillumina') - -Q 3 - #else if $query_seq.ext.startswith('pssm') - -Q 5 - #end if - - -f $lastal.f - -j $lastal.j - - -R $lastal.repeats_misc.uppercase_misc$lastal.repeats_misc.simple_repeat_misc - - #if $lastal.isprotein.schoring_schemes.score_matrix != 'scoreFile' - -p $lastal.isprotein.schoring_schemes.score_matrix - - -X $lastal.isprotein.schoring_schemes.score_opt.X - -x $lastal.isprotein.schoring_schemes.score_opt.x - -y $lastal.isprotein.schoring_schemes.score_opt.y - -z $lastal.isprotein.schoring_schemes.score_opt.z - -d $lastal.isprotein.schoring_schemes.score_opt.d - -e $lastal.isprotein.schoring_schemes.score_opt.e - - -a $lastal.isprotein.schoring_schemes.cost_opt.a - -b $lastal.isprotein.schoring_schemes.cost_opt.b - -A $lastal.isprotein.schoring_schemes.cost_opt.A - -B $lastal.isprotein.schoring_schemes.cost_opt.B - - -s $lastal.isprotein.s - #else if $lastal.isprotein.schoring_schemes.score_matrix == 'scoreFile' - -p $lastal.isprotein.schoring_schemes.scoreMatrixFile - #end if - - -D $lastal.evalue_opt.D - - -m $lastal.init_match_opt.m - -l $lastal.init_match_opt.l - -L $lastal.init_match_opt.L - -k $lastal.init_match_opt.k - -W $lastal.init_match_opt.W - - -S $lastal.misc_opt.S - -K $lastal.misc_opt.K - -C $lastal.misc_opt.C - -T $lastal.misc_opt.T - -n $lastal.misc_opt.n - -w $lastal.misc_opt.w - -u $lastal.misc_opt.u - -g $lastal.misc_opt.g - - -P \${GALAXY_SLOTS:-1} - - #if $db_opts.db_opts_input == 'db' - '${"'" "'".join(str($db_opts.database.fields.path).split(","))}' - #else if $db_opts.db_opts_input == 'lastdb' - 'db_files/lastdb' - #end if - - >'$outfile' - ]]></command> - - <inputs> - <expand macro="input_db"/> - <param name="query_seq" type="data" format="fasta,fasta.gz,fastq,fastq.gz,tabular" label="Query sequences"/> - - <section name="lastal" title="Lastal arguments" expanded="true"> - <param argument="-f" type="select" multiple="false" label="Output format"> - <option value="MAF" selected="true">MAF</option> - <option value="TAB">TAB</option> - <option value="BlastTab">BlastTab</option> - <option value="BlastTab+">BlastTab+</option> - </param> - <param argument="-j" type="select" multiple="false" label="Output type"> - <option value="0">Match counts</option> - <option value="1">Gapless</option> - <option value="2">Redundant gapped</option> - <option value="3" selected="true">Gapped</option> - <option value="4">Column ambiguity estimates</option> - <option value="5">Gamma-centroid</option> - <option value="6">LAMA</option> - <option value="7">Expected counts</option> - </param> - - <conditional name="isprotein"> - <param name="lastal_protein" type="select" multiple="false" label="The sequences are :"> - <option value="dna" selected="true">DNA</option> - <option value="prot">Proteins (-p)</option> - </param> - <when value="dna"> - <conditional name="schoring_schemes"> - <param name="score_matrix" argument="-p" type="select" multiple="false" label="Match/mismatch score matrix."> - <option value="AT77">AT77</option> - <option value="ATMAP">ATMAP</option> - <option value="BISF">BISF</option> - <option value="BISR">BISR</option> - <option value="BL62">BLOSUM62</option> - <option value="BL80" selected="true">BLOSUM80</option> - <option value="HOXD70">HOXD70</option> - <option value="MIQS">MIQS</option> - <option value="PAM10">PAM10</option> - <option value="PAM30">PAM30</option> - <option value="scoreFile">Other score matrix</option> - </param> - <when value="AT77"> - <expand macro="score_macro"/> - <expand macro="cost_macro" a="15" b="2"/> - </when> - <when value="ATMAP"> - <expand macro="score_macro"/> - <expand macro="cost_macro" a="24" b="6"/> - </when> - <when value="BISF"> - <expand macro="score_macro"/> - <expand macro="cost_macro" a="21" b="9"/> - </when> - <when value="BISR"> - <expand macro="score_macro"/> - <expand macro="cost_macro" a="21" b="9"/> - </when> - <when value="BL62"> - <expand macro="score_macro"/> - <expand macro="cost_macro" a="11" b="2"/> - </when> - <when value="BL80"> - <expand macro="score_macro"/> - <expand macro="cost_macro" a="7" b="1"/> - </when> - <when value="HOXD70"> - <expand macro="score_macro"/> - <expand macro="cost_macro" a="400" b="30"/> - </when> - <when value="MIQS"> - <expand macro="score_macro"/> - <expand macro="cost_macro" a="13" b="2"/> - </when> - <when value="PAM10"> - <expand macro="score_macro"/> - <expand macro="cost_macro" a="20" b="3"/> - </when> - <when value="PAM30"> - <expand macro="score_macro"/> - <expand macro="cost_macro" a="13" b="3"/> - </when> - <when value="scoreFile"> - <param name="scoreMatrixFile" type="data" format="txt" label="Score matrix file" /> - </when> - </conditional> - <param argument="-s" type="select" multiple="false" label="Strand"> - <option value="0">Reverse</option> - <option value="1">Forward</option> - <option value="2" selected="true">Both</option> - </param> - </when> - <when value="prot"> - <conditional name="schoring_schemes"> - <param name="score_matrix" argument="-p" type="select" multiple="false" label="Match/mismatch score matrix."> - <option value="AT77">AT77</option> - <option value="ATMAP">ATMAP</option> - <option value="BISF">BISF</option> - <option value="BISR">BISR</option> - <option value="BL62" selected="true">BLOSUM62</option> - <option value="BL80">BLOSUM80</option> - <option value="HOXD70">HOXD70</option> - <option value="MIQS">MIQS</option> - <option value="PAM10">PAM10</option> - <option value="PAM30">PAM30</option> - <option value="scoreFile">Other score matrix</option> - </param> - <when value="AT77"> - <expand macro="score_macro"/> - <expand macro="cost_macro" a="15" b="2"/> - </when> - <when value="ATMAP"> - <expand macro="score_macro"/> - <expand macro="cost_macro" a="24" b="6"/> - </when> - <when value="BISF"> - <expand macro="score_macro"/> - <expand macro="cost_macro" a="21" b="9"/> - </when> - <when value="BISR"> - <expand macro="score_macro"/> - <expand macro="cost_macro" a="21" b="9"/> - </when> - <when value="BL62"> - <expand macro="score_macro"/> - <expand macro="cost_macro" a="11" b="2"/> - </when> - <when value="BL80"> - <expand macro="score_macro"/> - <expand macro="cost_macro" a="7" b="1"/> - </when> - <when value="HOXD70"> - <expand macro="score_macro"/> - <expand macro="cost_macro" a="400" b="30"/> - </when> - <when value="MIQS"> - <expand macro="score_macro"/> - <expand macro="cost_macro" a="13" b="2"/> - </when> - <when value="PAM10"> - <expand macro="score_macro"/> - <expand macro="cost_macro" a="20" b="3"/> - </when> - <when value="PAM30"> - <expand macro="score_macro"/> - <expand macro="cost_macro" a="13" b="3"/> - </when> - <when value="scoreFile"> - <param name="scoreMatrixFile" type="data" format="txt" label="Score matrix file" /> - </when> - </conditional> - <param argument="-s" type="select" multiple="false" label="Strand"> - <option value="0">Reverse</option> - <option value="1" selected="true">Forward</option> - <option value="2">Both</option> - </param> - </when> - </conditional> - - <section name="repeats_misc" title="Specify lowercase-marking of repeats. (-R)" expanded="false"> - <param name="uppercase_misc" type="select" multiple="false" label="Input sequences to uppercase."> - <option value="0">Convert the input sequences to uppercase while reading them.(0)</option> - <option value="1" selected="true">Keep any lowercase in the input sequences.(1)</option> - </param> - <param name="simple_repeat_misc" type="select" multiple="false" label="Check for simple repeats."> - <option value="0" selected="true">Do not check for simple repeats.(0)</option> - <option value="1">Convert simple repeats to lowercase.(1)</option> - <option value="2">Convert simple DNA repeats to lowercase.(2)</option> - </param> - </section> - - <section name="evalue_opt" title="E-value options" expanded="false"> - <param argument="-D" type="integer" value="1000000" label="Query letters per random alignment (-D)"/> - <!--<param argument="-E" type="integer" value="1e+18" label="Maximum expected alignments per square giga"/>--> - </section> - - <section name="init_match_opt" title="Initial-match options" expanded="false"> - <param argument="-m" type="integer" value="10" min="1" label="Maximum initial matches per query position"/> - <param argument="-l" type="integer" value="1" min="1" label="Minimum length for initial matches"/> - <!-- Infinity --> - <param argument="-L" type="integer" value="999999999" min="1" label="Maximum length for initial matches"/> - <param argument="-k" type="integer" value="1" min="1" label="Use initial matches starting at every k-th position in each query"/> - <param argument="-W" type="integer" value="1" min="1" label="Use minimum positions in sliding windows of W consecutive positions"/> - </section> - - <section name="misc_opt" title="Miscellaneous options" expanded="false"> - <param argument="-S" type="select" multiple="false" label="Score matrix applies to forward strand of :"> - <option value="0" selected="true">Reference</option> - <option value="1">Query</option> - </param> - <param argument="-K" type="integer" value="0" min="0" label="Omit alignments whose query range lies in >= K others with > score"/> - <param argument="-C" type="integer" value="0" min="0" label="Omit gapless alignments in >= C others with > score-per-length"/> - <!--<param name="omit_gap" argument="-M" type="integer" value="" label="Find minimum-difference alignments (faster but cruder)"/>--> - - <param argument="-T" type="select" multiple="false" label="Type of alignment"> - <option value="0" selected="true">Local</option> - <option value="1">Overlap</option> - </param> - <param argument="-n" type="integer" value="10" min="0" label="Maximum gapless alignments per query position" help="Infinity if m=0"/> - <!--<param name="max_gap_align" argument="-N" type="integer" value="0" label="Stop after the first N alignments per query strand"/>--> - - <!-- Condition lastdb : 2 if lastdb -c and Q<5 --> - <param argument="-u" type="select" multiple="false" label="Mask lowercase during extensions."> - <option value="0" selected="true">Never.(0)</option> - <option value="1">Gapless.(1)</option> - <option value="2">Gapless+postmask.(2)</option> - <option value="3">Always.(3)</option> - </param> - <param argument="-w" type="integer" value="1000" min="0" label="Suppress repeats inside exact matches, offset by less or equal this distance. Use 0 to set this off" help="Use 0 to turn this off"/> - - <!-- https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi --> - <!-- Condition if ADN vs prot and -F --> - <param argument="-G" type="select" multiple="false" label="Genetic code."> - <option value="1" selected="true">Standard Code</option> - <option value="2">Vertebrate Mitochondrial Code</option> - <option value="3">Yeast Mitochondrial Code</option> - <option value="4">Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma</option> - <option value="5">Invertebrate Mitochondrial Code</option> - <option value="6">Ciliate, Dasycladacean and Hexamita Nuclear Code</option> - <option value="9">Echinoderm and Flatworm Mitochondrial Code</option> - <option value="10">Euplotid Nuclear Code</option> - <option value="11">Bacterial, Archaeal and Plant Plastid Code</option> - <option value="12">Alternative Yeast Nuclear Code</option> - <option value="13">Ascidian Mitochondrial Code</option> - <option value="14">Alternative Flatworm Mitochondrial Code</option> - <option value="16">Chlorophycean Mitochondrial Code</option> - <option value="21">Trematode Mitochondrial Code</option> - <option value="22">Scenedesmus obliquus Mitochondrial Code</option> - <option value="23">Thraustochytrium Mitochondrial Code</option> - <option value="24">Pterabranchia Mitochondrial Code</option> - <option value="25">Candidate Division SR1 and Gracilibacteria Code</option> - <option value="26">Pachysolen tannophilus Nuclear Code</option> - <option value="27">Karyorelict Nuclear Code</option> - <option value="28">Condylostoma Nuclear Code</option> - <option value="29">Mesodinium Nuclear Code</option> - <option value="30">Peritrich Nuclear Code</option> - <option value="31">Blastocrithidia Nuclear Code</option> - <option value="33">Cephalodiscidae Mitochondrial UAA-Tyr Code</option> - <!-- Add filename option with <repeat> --> - </param> - - <!--<param name="temperature" argument="-t" type="integer" value="1/lambda" label="Temperature for calculating probabilities"/>--> - <param argument="-g" type="integer" value="1" min="0" label="Gamma parameter for gamma-centroid and LAMA"/> - </section> - </section> - </inputs> - - <outputs> - <data name="outfile" format="maf" label="LAST align from ${on_string}" > - <change_format> - <when input="f" value="MAF" format="maf" /> - <when input="f" value="TAB" format="tabular" /> - <when input="f" value="BlastTab" format="tabular" /> - <when input="f" value="BlastTab+" format="tabular" /> - </change_format> - </data> - </outputs> - - <tests> - <test> - <conditional name="db_opts"> - <param name="db_opts_input" value="db"/> - <param name="database" value="humdb"/> - </conditional> - <param name="query_seq" value="fuguMito.fa.gz" ftype="fasta.gz"/> - <output name="outfile" ftype="maf" file="last_align_gen.maf" lines_diff="2"/> - </test> - <test> - <conditional name="db_opts"> - <param name="db_opts_input" value="db"/> - <param name="database" value="hedgdb"/> - </conditional> - <section name="lastal"> - <conditional name="isprotein"> - <param name="lastal_protein" value="prot"/> - </conditional> - </section> - <param name="query_seq" value="hedgehog_prot_drosophila.fa" ftype="fasta"/> - <output name="outfile" ftype="maf" file="last_align_prot.maf" lines_diff="2"/> - </test> - <test> - <conditional name="db_opts"> - <param name="db_opts_input" value="db"/> - <param name="database" value="humdb-sanger"/> - </conditional> - <param name="query_seq" value="fuguMito.fq.gz" ftype="fastqsanger.gz"/> - <section name="lastal"> - <param name="Q" value="1"/> - </section> - <output name="outfile" ftype="maf" file="last_align_fastq.maf" lines_diff="2"/> - </test> - </tests> - - <help>@LAST_HELP@</help> - <citations><expand macro="citations"/></citations> -</tool>
--- a/lastdb.xml Tue Aug 31 09:15:05 2021 +0000 +++ b/lastdb.xml Sat Nov 27 10:11:58 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="last_db" name="LASTdb" version="@LAST_CONDA_VERSION@+galaxy0" profile="20.01"> +<tool id="last_db" name="LASTdb" version="@TOOL_VERSION@+galaxy0" profile="20.01"> <description>prepares sequences for subsequent comparison and alignment using lastal.</description> <expand macro="bio_tools"/> @@ -7,7 +7,7 @@ </macros> <requirements> - <requirement type="package" version="@LAST_CONDA_VERSION@">last</requirement> + <requirement type="package" version="@TOOL_VERSION@">last</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[
--- a/lastdb.xml.orig Tue Aug 31 09:15:05 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,218 +0,0 @@ -<<<<<<< HEAD -<tool id="last_db" name="LASTdb" version="@LAST_CONDA_VERSION@+galaxy0" profile="20.01"> - -======= -<tool id="last_db" name="LASTdb" version="@LAST_CONDA_VERSION@+galaxy1" profile="18.01"> ->>>>>>> c37d72558 (add more bio.tool IDs) - <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="@LAST_CONDA_VERSION@">last</requirement> - </requirements> - - <command detect_errors="exit_code"><![CDATA[ - set -e -o pipefail; - - #if $input_files.ext.endswith('.gz') - zcat - #else - cat - #end if - '$input_files' | lastdb - - #if $input_files.ext.startswith('fasta') - -Q 0 - #else if $input_files.ext.startswith('fastqsanger') - -Q 1 - #else if $input_files.ext.startswith('fastqsolexa') - -Q 2 - #else if $input_files.ext.startswith('fastqillumina') - -Q 3 - #end if - $lastdb.sequences_type.protein - -a $lastdb.sequences_type.a - -R $lastdb.repeats.uppercase$lastdb.repeats.simple_repeat - $lastdb.repeats.sm_lower - -S $lastdb.lastdb_advanced.S - #if $lastdb.lastdb_advanced.seeds.u != '' - -u $lastdb.lastdb_advanced.seeds.u - #end if - -w $lastdb.lastdb_advanced.seeds.w - #if $lastdb.lastdb_advanced.seeds.W - -W $lastdb.lastdb_advanced.seeds.W - #end if - -m $lastdb.lastdb_advanced.seeds.m - -i $lastdb.lastdb_advanced.i - -C $lastdb.lastdb_advanced.C - -s \${GALAXY_MEMORY_MB:-2G} - -P \${GALAXY_SLOTS:-1} - 'lastdb' - - - && - - mkdir '$outfile.files_path' && - mv lastdb* '$outfile.files_path' - ]]></command> - - <inputs> - <param name="input_files" type="data" format="fasta,fasta.gz,fastq,fastq.gz" label="Reference(s) input files" /> - <section name="lastdb" title="Lastdb arguments" expanded="true"> - <conditional name="sequences_type"> - <param name="protein" type="select" multiple="false" label="The sequences are :"> - <option value="" selected="true">DNA</option> - <option value="-p">Proteins (-p)</option> - </param> - <when value=""> - <param argument="-a" type="text" value="ACGT" label="User-defined alphabet."/> - </when> - <when value="-p"> - <param argument="-a" type="text" value="ACDEFGHIKLMNPQRSTVWY" label="User-defined alphabet."/> - </when> - </conditional> - - <section name="repeats" title="Specify lowercase-marking of repeats. (-R)" expanded="false"> - <param name="uppercase" type="select" multiple="false" label="Convert the input sequences to uppercase while reading them."> - <option value="0">Convert the input sequences to uppercase while reading them. (0)</option> - <option value="1" selected="true">Keep any lowercase in the input sequences. (1)</option> - </param> - <param name="simple_repeat" type="select" multiple="false" label="Check for simple repeats."> - <option value="0" selected="true">Do not check for simple repeats.(0)</option> - <option value="1">Convert simple repeats to lowercase.(1)</option> - <option value="2">Convert simple DNA repeats to lowercase.(2)</option> - </param> - <param name="sm_lower" argument="-c" type="boolean" truevalue="-c" falsevalue="" checked="true" label="Soft-mask lowercase letters." help="This means that, when we compare these sequences to some other sequences using lastal, lowercase letters will be excluded from initial matches. This will apply to lowercase letters in both sets of sequences."/> - </section> - - <section name="lastdb_advanced" title="Advanced options" expanded="false"> - <param argument="-S" type="select" multiple="false" label="Strand"> - <option value="0">Reverse</option> - <option value="1" selected="true">Forward</option> - <option value="2">Both</option> - </param> - - <conditional name="seeds"> - <param argument="-u" type="select" multiple="false" label="Specify a seeding scheme."> - <option value="">Do not apply seeding scheme</option> - <option value="BISF">BISF</option> - <option value="BISR">BISR</option> - <option value="MAM4">MAM4</option> - <option value="MAM8">MAM8</option> - <option value="MURPHY10">MURPHY10</option> - <option value="NEAR">NEAR</option> - <option value="YASS" selected="true">YASS</option> - <!-- Add filename option --> - </param> - <when value=""/> - <when value="BISF"> - <expand macro="step_macro" step="2"/> - </when> - <when value="BISR"> - <expand macro="step_macro" step="2"/> - </when> - <when value="MAM4"> - <expand macro="step_macro" step="1"/> - </when> - <when value="MAM8"> - <expand macro="step_macro" step="1"/> - </when> - <when value="MURPHY10"> - <expand macro="step_macro" step="1"/> - </when> - <when value="NEAR"> - <expand macro="step_macro" step="1"/> - </when> - <when value="YASS"> - <expand macro="step_macro" step="1"/> - </when> - </conditional> - - <param argument="-i" type="integer" value="0" label="Minimum limit on initial matches per query position"/> - - <param argument="-C" type="select" multiple="false" label="Child table type"> - <option value="0" selected="true">None</option> - <option value="1">Byte-size</option> - <option value="2">Short-syze</option> - <option value="3">Full</option> - </param> - </section> - </section> - </inputs> - - <outputs> - <data name="outfile" format="lastdb"> - <discover_datasets pattern="__designation__" directory="ref_genome"/> - </data> - </outputs> - - <tests> - <test> - <param name="input_files" value="humanMito.fa.gz" ftype="fasta.gz"/> - <section name="lastdb"> - <section name="repeats"> - <param name="uppercase" value="0"/> - <param name="simple_repeat" value="1"/> - <param name="sm_lower" value="true"/> - </section> - </section> - <output name="outfile" compare="contains" file="humdb.lastdb" ftype="lastdb"> - <extra_files type="file" value="humdb.bck" name="lastdb.bck" compare="sim_size" delta="1"/> - <extra_files type="file" value="humdb.des" name="lastdb.des"/> - <extra_files type="file" value="humdb.prj" name="lastdb.prj" compare="sim_size" delta="2"/> - <extra_files type="file" value="humdb.sds" name="lastdb.sds"/> - <extra_files type="file" value="humdb.ssp" name="lastdb.ssp" compare="sim_size" delta="1"/> - <extra_files type="file" value="humdb.suf" name="lastdb.suf" compare="sim_size" delta="1"/> - <extra_files type="file" value="humdb.tis" name="lastdb.tis" compare="sim_size" delta="1"/> - </output> - </test> - <test> - <param name="input_files" value="hedgehog_prot_human.fa" ftype="fasta"/> - <section name="lastdb"> - <conditional name="sequences_type"> - <param name="protein" value="-p"/> - </conditional> - </section> - <section name="lastdb_advanced"> - <conditional name="seeds"> - <param name="u" value="MURPHY10"/> - </conditional> - </section> - <output name="outfile" compare="contains" file="hedgdb.lastdb" ftype="lastdb"> - <extra_files type="file" value="hedgdb.bck" name="lastdb.bck" compare="sim_size" delta="1"/> - <extra_files type="file" value="hedgdb.des" name="lastdb.des"/> - <extra_files type="file" value="hedgdb.prj" name="lastdb.prj"/> - <extra_files type="file" value="hedgdb.sds" name="lastdb.sds"/> - <extra_files type="file" value="hedgdb.ssp" name="lastdb.ssp" compare="sim_size" delta="1"/> - <extra_files type="file" value="hedgdb.suf" name="lastdb.suf" compare="sim_size" delta="1"/> - <extra_files type="file" value="hedgdb.tis" name="lastdb.tis" compare="sim_size" delta="1"/> - </output> - </test> - <test> - <param name="input_files" value="humanMito.fq.gz" ftype="fastqsanger.gz"/> - <section name="lastdb"> - <param name="Q" value="1"/> - <section name="repeats"> - <param name="uppercase" value="0"/> - <param name="simple_repeat" value="1"/> - <param name="sm_lower" value="true"/> - </section> - </section> - <output name="outfile" compare="contains" file="humdb-sanger.lastdb" ftype="lastdb"> - <extra_files type="file" value="humdb-sanger.bck" name="lastdb.bck" compare="sim_size" delta="1"/> - <extra_files type="file" value="humdb-sanger.des" name="lastdb.des"/> - <extra_files type="file" value="humdb-sanger.prj" name="lastdb.prj" lines_diff="2"/> - <extra_files type="file" value="humdb-sanger.sds" name="lastdb.sds"/> - <extra_files type="file" value="humdb-sanger.ssp" name="lastdb.ssp" compare="sim_size" delta="1"/> - <extra_files type="file" value="humdb-sanger.suf" name="lastdb.suf" compare="sim_size" delta="1"/> - <extra_files type="file" value="humdb-sanger.tis" name="lastdb.tis" compare="sim_size" delta="1"/> - </output> - </test> - </tests> - - <help>@LAST_HELP@</help> - <citations><expand macro="citations"/></citations> -</tool>
--- a/lastsplit.xml Tue Aug 31 09:15:05 2021 +0000 +++ b/lastsplit.xml Sat Nov 27 10:11:58 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="last_split" name="LAST-split" version="@LAST_CONDA_VERSION@+galaxy0" profile="20.01"> +<tool id="last_split" name="LAST-split" version="@TOOL_VERSION@+galaxy0" profile="20.01"> <description>finds "split alignments" (typically for DNA) or "spliced alignments" (typically for RNA).</description> <expand macro="bio_tools"/> @@ -7,7 +7,7 @@ </macros> <requirements> - <requirement type="package" version="@LAST_CONDA_VERSION@">last</requirement> + <requirement type="package" version="@TOOL_VERSION@">last</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[
--- a/lasttrain.xml Tue Aug 31 09:15:05 2021 +0000 +++ b/lasttrain.xml Sat Nov 27 10:11:58 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="last_train" name="LAST-train" version="@LAST_CONDA_VERSION@+galaxy0" profile="20.01"> +<tool id="last_train" name="LAST-train" version="@TOOL_VERSION@+galaxy0" profile="20.01"> <description>finds the rates (probabilities) of insertion, deletion, and substitutions between two sets of sequences.</description> <expand macro="bio_tools"/> @@ -7,7 +7,7 @@ </macros> <requirements> - <requirement type="package" version="@LAST_CONDA_VERSION@">last</requirement> + <requirement type="package" version="@TOOL_VERSION@">last</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[
--- a/macros_last.xml Tue Aug 31 09:15:05 2021 +0000 +++ b/macros_last.xml Sat Nov 27 10:11:58 2021 +0000 @@ -1,5 +1,5 @@ <macros> - <token name="@LAST_CONDA_VERSION@">1205</token> + <token name="@TOOL_VERSION@">1205</token> <token name="@LAST_HELP@"><![CDATA[ Documentation : http://last.cbrc.jp/
--- a/maf-convert.xml Tue Aug 31 09:15:05 2021 +0000 +++ b/maf-convert.xml Sat Nov 27 10:11:58 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="last_maf_convert" name="MAF-convert" version="@LAST_CONDA_VERSION@+galaxy0" profile="20.01"> +<tool id="last_maf_convert" name="MAF-convert" version="@TOOL_VERSION@+galaxy0" profile="20.01"> <description>read MAF-format alignments and write them in another format.</description> <expand macro="bio_tools"/> @@ -7,7 +7,7 @@ </macros> <requirements> - <requirement type="package" version="@LAST_CONDA_VERSION@">last</requirement> + <requirement type="package" version="@TOOL_VERSION@">last</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[
--- a/maf-convert.xml.orig Tue Aug 31 09:15:05 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,153 +0,0 @@ -<<<<<<< HEAD -<tool id="last_maf_convert" name="MAF-convert" version="@LAST_CONDA_VERSION@+galaxy0" profile="20.01"> - -======= -<tool id="last_maf_convert" name="MAF-convert" version="@LAST_CONDA_VERSION@+galaxy0" profile="18.01"> ->>>>>>> c37d72558 (add more bio.tool IDs) - <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="@LAST_CONDA_VERSION@">last</requirement> - </requirements> - <command detect_errors="exit_code"><![CDATA[ - maf-convert - - $maf_convert.output_type.output_format - - $maf_convert.noheader - - #if $maf_convert.output_type.output_format == 'psl' - $maf_convert.output_type.protein - -j $maf_convert.output_type.j - #end if - - #if $maf_convert.output_type.output_format == 'sam' - $maf_convert.output_type.sam_file.dictionary - #if $maf_convert.output_type.sam_file.dictionary == '-d' - -f $maf_convert.output_type.sam_file.f - #end if - #if $maf_convert.output_type.readfile != '' - -r $maf_convert.output_type.r - #end if - #end if - - #if $maf_convert.output_type.output_format == 'blast' or $maf_convert.output_type.output_format == 'html' - -l $maf_convert.output_type.l - #end if - - '$maf_file' - - > '$outfile' - - ]]></command> - <inputs> - <param name="maf_file" type="data" format="maf" label="MAF file to convert" /> - - <section name="maf_convert" title="MAF-convert arguments" expanded="true"> - - <param name="noheader" argument="-n" type="boolean" truevalue="-n" falsevalue="" checked="false" label="No header." help="Omit any header lines from the output"/> - - <conditional name="output_type"> - <param name="output_format" type="select" multiple="false" label="Output format"> - <option value="axt">axt</option> - <option value="blast">blast</option> - <option value="blasttab">blasttab</option> - <option value="chain">chain</option> - <option value="html">html</option> - <option value="psl" selected="true">psl</option> - <option value="sam">sam</option> - <option value="tab">tab</option> - </param> - <when value="axt"/> - <when value="blast"> - <param argument="-l" type="integer" value="60" label="Line length"/> - </when> - <when value="blasttab"/> - <when value="chain"/> - <when value="html"> - <param argument="-l" type="integer" value="60" label="Line length"/> - </when> - <when value="psl"> - <param name="protein" argument="-p" type="boolean" truevalue="-p" falsevalue="" checked="false" label="Protein alignments." /> - <param argument="-j" type="integer" value="1" label="Join neighboring alignments" help="Join neighboring alignments if they are co-linear and separated by at most N letters."/> - </when> - <when value="sam"> - <conditional name="sam_file"> - <param name="dictionary" argument="-d" type="select" label="Include dictionary of sequence lengths in sam format"> - <option value="-d">Yes</option> - <option value="" selected="true">No</option> - </param> - <when value=""/> - <when value="-d"> - <param argument="-f" type="data" format="dict" label="Get a sequence dictionary from DICTFILE" /> - </when> - </conditional> - <param argument="-r" type="text" value="" label="Specify read group information" help="Example: 'ID:1 PL:ILLUMINA SM:mysample'"/> - </when> - <when value="tab"/> - </conditional> - </section> - </inputs> - - <outputs> - <data format="maf" name="outfile" label="${on_string} to ${maf_convert.output_type.output_format}"> - <change_format> - <when input="maf_convert.output_type.output_format" value="axt" format="axt" /> - <when input="maf_convert.output_type.output_format" value="blast" format="blastxml" /> - <when input="maf_convert.output_type.output_format" value="blasttab" format="blastxml" /> - <when input="maf_convert.output_type.output_format" value="chain" format="txt" /> - <when input="maf_convert.output_type.output_format" value="html" format="html" /> - <when input="maf_convert.output_type.output_format" value="psl" format="tabular" /> - <when input="maf_convert.output_type.output_format" value="sam" format="sam" /> - <when input="maf_convert.output_type.output_format" value="tab" format="tabular" /> - </change_format> - </data> - </outputs> - - <tests> - <test> - <param name="maf_file" value="last_align_train_gen.maf" ftype="maf"/> - <section name="maf_convert"> - <conditional name="output_type"> - <param name="output_format" value="axt"/> - </conditional> - </section> - <output name="outfile" file="outfile_convert.axt"/> - </test> - <test> - <param name="maf_file" value="last_align_train_gen.maf" ftype="maf"/> - <section name="maf_convert"> - <conditional name="output_type"> - <param name="output_format" value="blast"/> - </conditional> - </section> - <output name="outfile" file="outfile_convert.blast"/> - </test> - <test> - <param name="maf_file" value="last_align_train_gen.maf" ftype="maf"/> - <section name="maf_convert"> - <conditional name="output_type"> - <param name="output_format" value="html"/> - </conditional> - </section> - <output name="outfile" file="outfile_convert.html"/> - </test> - <test> - <param name="maf_file" value="last_align_train_gen.maf" ftype="maf"/> - <section name="maf_convert"> - <conditional name="output_type"> - <param name="output_format" value="tab"/> - </conditional> - </section> - <output name="outfile" file="outfile_convert.tab"/> - </test> - </tests> - - <help><![CDATA[ - This script reads alignments in maf format, and writes them in another format. It can write them in these formats: axt, blast, blasttab, chain, html, psl, sam, tab. - ]]></help> - <citations><expand macro="citations"/></citations> -</tool>