Mercurial > repos > mbernt > maxbin2
diff maxbin2.xml @ 2:6a638de7915c draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maxbin2/ commit 08beeabf7a8e91d0e95f5cdb71249dd6efe2bd46"
| author | iuc |
|---|---|
| date | Tue, 29 Oct 2019 08:45:20 -0400 |
| parents | 864279a0d64b |
| children | cfd50144a871 |
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--- a/maxbin2.xml Tue Oct 16 10:28:16 2018 -0400 +++ b/maxbin2.xml Tue Oct 29 08:45:20 2019 -0400 @@ -1,6 +1,10 @@ -<tool id="maxbin2" name="MaxBin2" version="2.2.4_galaxy1"> +<tool id="maxbin2" name="MaxBin2" version="@MAXBIN_VERSION@+galaxy1"> + <description>clusters metagenomic contigs into bins</description> + <macros> + <token name="@MAXBIN_VERSION@">2.2.7</token> + </macros> <requirements> - <requirement type="package" version="2.2.4">maxbin2</requirement> + <requirement type="package" version="@MAXBIN_VERSION@">maxbin2</requirement> </requirements> <version_command><![CDATA[run_MaxBin.pl -version | head -n 1]]></version_command> <command detect_errors="exit_code"><![CDATA[ @@ -47,9 +51,11 @@ && tar -xf out.marker_of_each_bin.tar.gz - ## redirect the idba out and err file content to stdout and err + ## redirect the idba out and err file content to stdout and err + ## since this is also wanted in case the error case ';' is used here to + ## separate commands #if $intype_cond.intype_select == 'rds' and $intype_cond.reassembly != "" - && echo "==== IDBA stdout ====" + ; echo "==== IDBA stdout ====" && cat out.idba.out && echo "==== IDBA stderr ====" 1>&2 && cat out.idba.err 1>&2 @@ -63,11 +69,12 @@ <option value="abdc">Abundances</option> </param> <when value="rds"> - <param name="reads" argument="-read/-read2/..." type="data" format="fasta,fastq" multiple="true" label="Reads file(s)"/> - <param argument="--reassembly" type="boolean" truevalue="-reassembly" falsevalue="" checked="false" label="" help="Reassembly option is still highly experimental. To use this function, you need to feed MaxBin interleaved paired-end fastq or fasta file." /> + <param name="reads" type="data" format="fasta,fastq" multiple="true" label="Reads file(s)" help="(-read/-read2/...)"/> + <param name="output_abundances" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Output abundances" help="" /> + <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." /> </when> <when value="abdc"> - <param name="abund" argument="-abund/-abund2/..." type="data" format="tabular" multiple="true" label="Abundance file(s)"/> + <param name="abund" type="data" format="tabular" multiple="true" label="Abundance file(s)" help="(-abund/-abund2/...)" /> </when> </conditional> <conditional name="adv_cond"> @@ -79,8 +86,11 @@ <when value="yes"> <param argument="-min_contig_length" type="integer" min="0" value="1000" label="minimum contig length" /> <param argument="-max_iteration" type="integer" min="0" value="50" label="Maximum Expectation-Maximization algorithm iteration number" /> - <param argument="-prob_threshold" type="float" min="0" max="1.0" value="0.9" label="Probability threshold for EM final classification" /> - <param name="plotmarker" type="boolean" truevalue="-plotmarker" falsevalue="" checked="false" label="Generate visualization of the marker gene presence numbers" /> + <param argument="-prob_threshold" type="float" min="0" max="1.0" value="0.5" label="Probability threshold for EM final classification" /> + <param argument="-plotmarker" type="boolean" truevalue="-plotmarker" falsevalue="" checked="false" label="Generate visualization of the marker gene presence numbers" /> + <param name="output_marker" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Output marker gene presence for bins table" /> + <param name="output_markers" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Output marker genes for each bin as fasta" /> + <param name="output_log" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Output log" /> <param argument="-markerset" type="select" label="Marker gene set"> <option value="107" selected="true">107 marker genes present in >95% of bacteria</option> <option value="40">40 marker gene sets that are universal among bacteria and archaea</option> @@ -89,25 +99,34 @@ </conditional> </inputs> <outputs> + <!-- default outputs --> <collection name="bins" type="list" label="${tool.name} on ${on_string} (bins)"> <discover_datasets pattern="out.(?P<designation>[0-9]+).fasta" format="fasta" visible="false" /> </collection> + <data name="noclass" format="fasta" label="${tool.name} on ${on_string} (unclassified sequences)" from_work_dir="out.noclass"/> + <data name="toshort" format="fasta" label="${tool.name} on ${on_string} (to short sequences)" from_work_dir="out.tooshort"/> <data name="summary" format="tabular" label="${tool.name} on ${on_string} (summary)" from_work_dir="out.summary"/> - <data name="log" format="txt" label="${tool.name} on ${on_string} (log)" from_work_dir="out.log"/> + + <!-- optional outputs --> + <data name="log" format="txt" label="${tool.name} on ${on_string} (log)" from_work_dir="out.log"> + <filter>adv_cond['adv_select']=='yes' and adv_cond['output_log']</filter> + </data> + <data name="marker" format="tabular" label="${tool.name} on ${on_string} (marker gene presence)" from_work_dir="out.marker"> + <filter>adv_cond['adv_select']=='yes' and adv_cond['output_marker']</filter> + </data> <data name="abundout" format="tabular" label="${tool.name} on ${on_string} (abundances)" from_work_dir="out.abund1"> - <filter>intype_cond['intype_select']=='rds'</filter> + <filter>intype_cond['intype_select']=='rds' and intype_cond['output_abundances']</filter> </data> - <data name="marker" format="tabular" label="${tool.name} on ${on_string} (marker gene presence)" from_work_dir="out.marker"/> <data name="plot" format="pdf" label="${tool.name} on ${on_string} (marker gene presence plot)" from_work_dir="out.marker.pdf"> <filter>adv_cond['adv_select']=='yes' and adv_cond['plotmarker']</filter> </data> - <data name="noclass" format="fasta" label="${tool.name} on ${on_string} (unclassified sequences)" from_work_dir="out.noclass"/> - <data name="toshort" format="fasta" label="${tool.name} on ${on_string} (to short sequences)" from_work_dir="out.tooshort"/> <collection name="markers" type="list" label="${tool.name} on ${on_string} (markers prediced for bins)"> <discover_datasets pattern="out.(?P<designation>[0-9]+).marker.fasta" format="fasta" visible="false" /> + <filter>adv_cond['adv_select']=='yes' and adv_cond['output_markers']</filter> </collection> + <!-- additional output in case of reassembly --> - <collection name="reassembly_bins" type="list" label="${tool.name} on ${on_string} (reassembly bins)"> + <collection name="reassembly_bins" type="list" label="${tool.name} on ${on_string} (reassembly bins)"> <discover_datasets directory="out.reassem" pattern="out.(?P<designation>[0-9]+).fasta" format="fasta" visible="false" /> <filter>intype_cond['intype_select']=='rds' and intype_cond['reassembly']</filter> </collection> @@ -123,11 +142,11 @@ </data> </outputs> <tests> - <test><!-- test w contigs and reads as input --> + <test expect_num_outputs="4"><!-- test w contigs and reads as input --> <param name="contig" value="Bin_Sample3_contigs.fasta" ftype="fasta" /> <conditional name="intype_cond"> <param name="intype_select" value="rds"/> - <param name="reads" value="interleavedPE_unmapped_Sample3_total.fasta" ftype="fasta"/> + <param name="reads" value="interleavedPE_unmapped_Sample3_small.fasta" ftype="fasta"/> </conditional> <conditional name="adv_cond"> <param name="adv_select" value="no"/> @@ -137,16 +156,41 @@ <element name="002" file="1/out.002.fasta" ftype="fasta"/> </output_collection> <output name="summary" file="1/out.summary" ftype="tabular" /> - <output name="log" file="1/out.log" ftype="txt" compare="diff" lines_diff="17" /> + <output name="noclass" file="1/out.noclass" ftype="fasta" /> + <output name="toshort" file="1/out.tooshort" ftype="fasta" /> + </test> + <!-- test w contigs and reads as input test for optional outputs --> + <test expect_num_outputs="9"> + <param name="contig" value="Bin_Sample3_contigs.fasta" ftype="fasta" /> + <conditional name="intype_cond"> + <param name="intype_select" value="rds"/> + <param name="reads" value="interleavedPE_unmapped_Sample3_small.fasta" ftype="fasta"/> + <param name="output_abundances" value="true" /> + </conditional> + <conditional name="adv_cond"> + <param name="adv_select" value="yes"/> + <param name="plotmarker" value="true" /> + <param name="output_marker" value="true" /> + <param name="output_markers" value="true" /> + <param name="output_log" value="true" /> + </conditional> + <output_collection name="bins" type="list" count="2"> + <element name="001" file="1/out.001.fasta" ftype="fasta"/> + <element name="002" file="1/out.002.fasta" ftype="fasta"/> + </output_collection> + <output name="summary" file="1/out.summary" ftype="tabular" /> + <output name="noclass" file="1/out.noclass" ftype="fasta" /> + <output name="toshort" file="1/out.tooshort" ftype="fasta" /> + <output name="log" file="1/out.log" ftype="txt" compare="diff" lines_diff="21" /> <output name="abundout" file="1/out.abund1" ftype="tabular" /> <output name="marker" file="1/out.marker" ftype="tabular" /> - <output name="noclass" file="1/out.noclass" ftype="fasta" /> - <output name="toshort" file="1/out.tooshort" ftype="fasta" /> + <output name="plot" file="1/out.marker.pdf" ftype="pdf" compare="sim_size" /> <output_collection name="markers" type="list" count="1"> <element name="001" file="1/out.001.marker.fasta" ftype="fasta"/> </output_collection> </test> - <test><!--test w contigs and abundances as input + advanced options --> + <!--test w contigs and abundances as input + advanced options --> + <test expect_num_outputs="5"> <param name="contig" value="Bin_Sample3_contigs.fasta" ftype="fasta" /> <conditional name="intype_cond"> <param name="intype_select" value="abdc"/> @@ -165,20 +209,16 @@ <element name="002" file="2/out.002.fasta" ftype="fasta"/> </output_collection> <output name="summary" file="2/out.summary" ftype="tabular" /> - <output name="log" file="2/out.log" ftype="txt" compare="diff" lines_diff="17" /> - <output name="marker" file="2/out.marker" ftype="tabular" /> - <output name="plot" file="2/out.marker.pdf" ftype="pdf" compare="sim_size" /> <output name="noclass" file="2/out.noclass" ftype="fasta" /> <output name="toshort" file="2/out.tooshort" ftype="fasta" /> - <output_collection name="markers" type="list" count="1"> - <element name="001" file="2/out.001.marker.fasta" ftype="fasta"/> - </output_collection> + <output name="plot" file="2/out.marker.pdf" ftype="pdf" compare="sim_size" /> </test> - <test><!-- test w contigs and reads as input + reassembly--> + <!-- test w contigs and reads as input + reassembly--> + <test expect_num_outputs="8"> <param name="contig" value="Bin_Sample3_contigs.fasta" ftype="fasta" /> <conditional name="intype_cond"> <param name="intype_select" value="rds"/> - <param name="reads" value="interleavedPE_unmapped_Sample3_total.fasta" ftype="fasta"/> + <param name="reads" value="interleavedPE_unmapped_Sample3_small.fasta" ftype="fasta"/> <param name="reassembly" value="-reassembly"/> </conditional> <conditional name="adv_cond"> @@ -189,14 +229,8 @@ <element name="002" file="3/out.002.fasta" ftype="fasta"/> </output_collection> <output name="summary" file="3/out.summary" ftype="tabular" /> - <output name="log" file="3/out.log" ftype="txt" compare="diff" lines_diff="17" /> - <output name="abundout" file="3/out.abund1" ftype="tabular" /> - <output name="marker" file="3/out.marker" ftype="tabular" /> <output name="noclass" file="3/out.noclass" ftype="fasta" /> <output name="toshort" file="3/out.tooshort" ftype="fasta" /> - <output_collection name="markers" type="list" count="1"> - <element name="001" file="3/out.001.marker.fasta" ftype="fasta"/> - </output_collection> <output_collection name="reassembly_bins" type="list" count="2"> <element name="001" file="3/out.reassem/out.001.fasta" ftype="fasta"/> <element name="002" file="3/out.reassem/out.002.fasta" ftype="fasta"/> @@ -215,7 +249,6 @@ nucleotide composition information and contig abundance information to do achieve binning through an Expectation-Maximization algorithm. - **Input**: MaxBin need the contigs and contig abundance information. The contig abundance @@ -258,15 +291,13 @@ This is an experimental feature of MaxBin. It calls for each read bin IDBA_UD with the pre_correction parameter. Of course this IDBA_UD call can be done also with the corresponding Galaxy tool + +** More information ** + +https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html + ]]></help> <citations> <citation type="doi">10.1093/bioinformatics/btv638</citation> - <citation type="bibtex"> -@misc{renameTODO, - author = {LastTODO, FirstTODO}, - year = {TODO}, - title = {TODO}, - url = {https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html}, -}</citation> </citations> </tool>