| Previous changeset 4:4ef88f9a195d (2020-11-18) Next changeset 6:2bc40bfbcfb4 (2023-10-16) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit e5b086199e53e32ffdf46ac6ba36c43f8ef6db26 |
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modified:
maxbin2.xml |
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| diff -r 4ef88f9a195d -r 8a0473eb465e maxbin2.xml --- a/maxbin2.xml Wed Nov 18 10:42:37 2020 +0000 +++ b/maxbin2.xml Fri Jun 17 17:27:40 2022 +0000 |
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| b'@@ -1,157 +1,202 @@\n-<tool id="maxbin2" name="MaxBin2" version="@MAXBIN_VERSION@+galaxy2">\n+<tool id="maxbin2" name="MaxBin2" version="@MAXBIN_VERSION@+galaxy3">\n <description>clusters metagenomic contigs into bins</description>\n+ <xrefs>\n+ <xref type="bio.tools">masigpro</xref>\n+ </xrefs>\n <macros>\n <token name="@MAXBIN_VERSION@">2.2.7</token>\n+ <xml name="contig">\n+ <param argument="-contig" type="data" format="fasta,fasta.gz" label="Contig file"/>\n+ </xml>\n+ <xml name="input_type">\n+ <param name="type" type="select" label="Input type">\n+ <option value="reads" selected="true">Sequencing Reads</option>\n+ <option value="abund">Abundances</option>\n+ </param>\n+ </xml>\n+ <xml name="reads_extra_params">\n+ <param name="output_abundances" type="boolean" checked="false" label="Output abundances" help="" />\n+ <param argument="--reassembly" type="boolean" truevalue="-reassembly" falsevalue="" checked="false" label="Reassembly" help="Reassembly option is still highly experimental. To use this function, you need to feed MaxBin interleaved paired-end fastq or fasta file." />\n+ </xml>\n </macros>\n <requirements>\n <requirement type="package" version="@MAXBIN_VERSION@">maxbin2</requirement>\n </requirements>\n <version_command><![CDATA[run_MaxBin.pl -version | head -n 1]]></version_command>\n <command detect_errors="exit_code"><![CDATA[\n- ## generate read or abundance files\t\n- #if $intype_cond.intype_select == \'rds\':\n- #for $r in $intype_cond.reads\n+## generate read or abundance files\n+#if $assembly.inputs.type == \'reads\'\n+ #if $assembly.type == \'individual\'\n+echo \'$assembly.inputs.reads\' >> reads_list &&\n+ #else\n+ #for $r in $assembly.inputs.reads\n #if $r\n- echo \'$r\' >> reads_list &&\n+echo \'$r\' >> reads_list &&\n #end if\n #end for\n- #else if $intype_cond.intype_select == \'abdc\':\n- #for $a in $intype_cond.abund\n+ #end if\n+#else if $assembly.inputs.type == \'abund\'\n+ #if $assembly.type == \'individual\'\n+echo \'$assembly.inputs.abund\' >> abund_list &&\n+ #else\n+ #for $a in $assembly.inputs.abund\n #if $a\n- echo \'$a\' >> abund_list &&\n+echo \'$a\' >> abund_list &&\n #end if\n #end for\n #end if\n+#end if\n \n- ## in case of reassembly the IBDA out and err is appended\n- ## to differentiate this a header is added also befor the\n- ## MaxBin2 outputs\n- #if $intype_cond.intype_select == \'rds\' and $intype_cond.reassembly != ""\n- echo "==== MaxBin2 stdout ====" &&\n- echo "==== MaxBin2 stderr ====" 1>&2 &&\n- #end if\n+## in case of reassembly the IBDA out and err is appended\n+## to differentiate this a header is added also befor the\n+## MaxBin2 outputs\n+#if $assembly.inputs.type == \'reads\' and $assembly.inputs.reassembly != ""\n+echo "==== MaxBin2 stdout ====" &&\n+echo "==== MaxBin2 stderr ====" 1>&2 &&\n+#end if\n \n- run_MaxBin.pl\n+run_MaxBin.pl\n -contig \'$contig\'\n -out out\n- #if $intype_cond.intype_select == \'rds\':\n- -reads_list reads_list\n- $intype_cond.reassembly\n- #else if $intype_cond.intype_select == \'abdc\':\n- -abund_list abund_list\n- #end if\n- #if $adv_cond.adv_select == \'yes\':\n- -min_contig_length $adv_cond.min_contig_length\n- -max_iteration $adv_cond.max_iteration\n- -prob_threshold $adv_cond.prob_threshold\n- $adv_cond.plotmarker\n- -markerset $adv_cond.markerset\n- #end if\n+#if $assembly.inputs.type == \'reads\':\n+ -reads_list reads_list\n+ $assembly.inputs.reassembly\n+#else if $assembly.inputs.type == \'abund\':\n+ -abund_list abund_list\n+#end if\n+ -min_contig_length $adv.min_contig_length\n+ -max_iteration $adv.max_iteration\n+ -prob_threshold $adv.prob_threshold\n+ $output.plotmarker\n+ -markerset $output.markers'..b'tional>\n+ </section>\n <output_collection name="bins" type="list" count="2">\n <element name="001" file="2/out.001.fasta" ftype="fasta"/>\n <element name="002" file="2/out.002.fasta" ftype="fasta"/>\n@@ -217,14 +289,27 @@\n <!-- test w contigs and reads as input + reassembly-->\n <test expect_num_outputs="8">\n <param name="contig" value="Bin_Sample3_contigs.fasta" ftype="fasta" />\n- <conditional name="intype_cond">\n- <param name="intype_select" value="rds"/>\n- <param name="reads" value="interleavedPE_unmapped_Sample3_small.fasta" ftype="fasta"/>\n- <param name="reassembly" value="-reassembly"/>\n+ <conditional name="assembly">\n+ <param name="type" value="individual"/>\n+ <conditional name="inputs">\n+ <param name="type" value="reads"/>\n+ <param name="reads" value="interleavedPE_unmapped_Sample3_small.fasta" ftype="fasta"/>\n+ <param name="output_abundances" value="false"/>\n+ <param name="reassembly" value="-reassembly"/>\n+ </conditional>\n </conditional>\n- <conditional name="adv_cond">\n- <param name="adv_select" value="no"/>\n- </conditional>\n+ <section name="adv">\n+ <param name="min_contig_length" value="1000"/>\n+ <param name="max_iteration" value="50"/>\n+ <param name="prob_threshold" value="0.5"/>\n+ </section>\n+ <section name="output">\n+ <param name="plotmarker" value=""/>\n+ <param name="marker" value="false"/>\n+ <param name="markers" value="false" />\n+ <param name="log" value="false"/>\n+ <param name="markerset" value="107"/>\n+ </section>\n <output_collection name="bins" type="list" count="2">\n <element name="001" file="3/out.001.fasta" ftype="fasta"/>\n <element name="002" file="3/out.002.fasta" ftype="fasta"/>\n@@ -233,15 +318,31 @@\n <output name="noclass" file="3/out.noclass" ftype="fasta" />\n <output name="toshort" file="3/out.tooshort" ftype="fasta" />\n <output_collection name="reassembly_bins" type="list" count="2">\n- <element name="001" file="3/out.reassem/out.001.fasta" ftype="fasta"/>\n- <element name="002" file="3/out.reassem/out.002.fasta" ftype="fasta"/>\n+ <element name="001" ftype="fasta">\n+ <assert_contents>\n+ <has_text text=">scaffold_0"/>\n+ <has_text text=">scaffold_523"/>\n+ </assert_contents>\n+ </element>\n+ <element name="002" ftype="fasta">\n+ <assert_contents>\n+ <has_text text=">scaffold_0"/>\n+ <has_text text=">scaffold_523"/>\n+ </assert_contents>\n+ </element>\n </output_collection>\n <output_collection name="reassembly_reads" type="list" count="2">\n <element name="001" file="3/out.reassem/out.reads.001" ftype="fasta"/>\n <element name="002" file="3/out.reassem/out.reads.002" ftype="fasta"/>\n </output_collection>\n <output name="reassembly_noclass" file="3/out.reassem/out.reads.noclass" ftype="fasta" />\n- <output name="reassembly_n50" file="3/out.reassem/N50.txt" ftype="txt" />\n+ <output name="reassembly_n50" ftype="txt">\n+ <assert_contents>\n+ <has_text text="N50 before reassem"/>\n+ <has_text text="out.002.fasta"/>\n+ <has_text text="2878"/>\n+ </assert_contents>\n+ </output>\n </test>\n </tests>\n <help><![CDATA[\n' |