Mercurial > repos > iuc > purge_dups
changeset 1:29151e779524 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 6b395e598c4a02bb193895da5a2d9dd4240b1848"
| author | iuc |
|---|---|
| date | Tue, 09 Mar 2021 18:25:07 +0000 |
| parents | 8ec117da1796 |
| children | 17b378303f2d |
| files | purge_dups.xml test-data/test.paf.gz |
| diffstat | 2 files changed, 56 insertions(+), 7 deletions(-) [+] |
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--- a/purge_dups.xml Fri Feb 05 17:52:51 2021 +0000 +++ b/purge_dups.xml Tue Mar 09 18:25:07 2021 +0000 @@ -1,14 +1,17 @@ -<tool id="purge_dups" name="Purge haplotigs" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> - <description>and overlaps in an assembly based on read depth</description> +<tool id="purge_dups" name="Purge overlaps" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> + <description>and haplotigs in an assembly based on read depth (purge_dups)</description> <macros> <token name="@TOOL_VERSION@">1.2.5</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> </macros> <requirements> <requirement type="package" version="@TOOL_VERSION@">purge_dups</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ #if $function_select.functions == "purge_dups": + #if $function_select.input.is_of_type("paf"): + gzip -c '$function_select.input' > ./input.paf.gz && + #end if purge_dups #if $function_select.coverage: -c '$function_select.coverage' @@ -43,7 +46,11 @@ #if $function_select.max_extend: -E $function_select.max_extend #end if - '$function_select.input' > dups.bed 2> purge_dups.log + #if $function_select.input.is_of_type("paf"): + 'input.paf.gz' > dups.bed 2> purge_dups.log + #else: + '${function_select.input}' > dups.bed 2> purge_dups.log + #end if #else if $function_select.functions == "split_fa": split_fa #if $function_select.split: @@ -51,6 +58,9 @@ #end if '$function_select.input' > split.fasta #else if $function_select.functions == "pbcstat": + #if $function_select.input.is_of_type("paf"): + gzip -c '$function_select.input' > ./input.paf.gz && + #end if pbcstat #if $function_select.max_cov: -M $function_select.max_cov @@ -65,7 +75,11 @@ -l $function_select.flank #end if $function_select.primary_alignments - '$function_select.input' + #if $function_select.input.is_of_type("paf"): + 'input.paf.gz' + #else: + '${function_select.input}' + #end if #else if $function_select.functions == "ngscstat": ngscstat #if $function_select.min_align_qual: @@ -123,7 +137,7 @@ <option value="get_seqs">obtain seqeuences after purging</option> </param> <when value="purge_dups"> - <param name="input" type="data" format="paf" label="PAF input file"/> + <param name="input" type="data" format="paf,paf.gz" label="PAF input file"/> <param name="coverage" type="data" format="tabular" optional="true" argument="-c" label="Base-level coverage file" /> <param name="cutoffs" type="data" format="tabular" label ="Cutoffs file" optional="true" argument="-T"/> <param name="min_bad" type="float" min="0" max="1" argument="-f" optional="true" label="Minimum fraction of haploid/diploid/bad/repetitive bases in a sequence" help="Default = 0.8"/> @@ -149,7 +163,7 @@ <param name="split" type="boolean" truevalue="-n" falsevalue="" checked="false" label="Base-level coverage file" /> </when> <when value="pbcstat"> - <param name="input" type="data" format="paf" label="PAF input file"/> + <param name="input" type="data" format="paf,paf.gz" label="PAF input file"/> <param name="max_cov" type="integer" label="Maximum coverage" argument="-M" optional="true"/> <param name="min_map_ratio" argument="-f" type="float" min="0" max="1" value="0" label="Minimum mapping length ratio"/> <param name="min_map_qual" type="integer" argument="-q" optional="true" label="Minimum mapping quality"/> @@ -253,6 +267,27 @@ </conditional> <output name="purge_dups_bed" value="purge_dups_out.bed"/> </test> + <!-- Purge dups gzip --> + <test expect_num_outputs="2"> + <conditional name="function_select"> + <param name="functions" value="purge_dups"/> + <param name="input" value="test.paf.gz" ftype="paf.gz"/> + <param name="coverage" value="test.cov" ftype="tabular"/> + <param name="cutoffs" value="cutoffs.tsv" ftype="tabular"/> + <param name="min_bad" value="0.01"/> + <param name="min_align" value="10"/> + <param name="min_match" value="100"/> + <param name="min_chain" value="1"/> + <param name="max_gap" value="1000"/> + <conditional name="double_chain"> + <param name="chaining_rounds" value="two"/> + <param name="max_gap_2" value="1001"/> + </conditional> + <param name="min_chain_score" value="1"/> + <param name="max_extend" value="100"/> + </conditional> + <output name="purge_dups_bed" value="purge_dups_out.bed"/> + </test> <!-- Split fa --> <test expect_num_outputs="1"> <conditional name="function_select"> @@ -276,6 +311,20 @@ <output name="pbcstat_cov" value="out.cov"/> <output name="pbcstat_wig" value="out.wig"/> </test> + <!-- pbcstat gzip --> + <test expect_num_outputs="3"> + <conditional name="function_select"> + <param name="functions" value="pbcstat"/> + <param name="input" value="test.paf.gz" ftype="paf.gz"/> + <param name="max_cov" value="1000"/> + <param name="min_map_ratio" value="0.01"/> + <param name="min_map_qual" value="1"/> + <param name="flank" value="1"/> + <param name="primary_alignments" value="-p"/> + </conditional> + <output name="pbcstat_cov" value="out.cov"/> + <output name="pbcstat_wig" value="out.wig"/> + </test> <!-- ngscstat --> <test expect_num_outputs="2"> <conditional name="function_select">