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comparison metaphlan.xml @ 5:6dee4abadccb draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit f3a89af137b13715f9fb13383577aceb2c445ce6
author iuc
date Sat, 03 Dec 2022 10:43:21 +0000
parents ff8f55893e7d
children 2131d7dca455
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4:a16313517e55 5:6dee4abadccb
105 #end if 105 #end if
106 106
107 #if $inputs.db.db_selector == "history" 107 #if $inputs.db.db_selector == "history"
108 mkdir 'ref_db' 108 mkdir 'ref_db'
109 && 109 &&
110 bowtie2-build '$inputs.db.bowtie2db' 'ref_db/custom_db' 110 bowtie2-build --large-index '$inputs.db.bowtie2db' 'ref_db/custom_db'
111 && 111 &&
112 python '$__tool_directory__/customizemetadata.py' 112 python '$__tool_directory__/customizemetadata.py'
113 transform_json_to_pkl 113 transform_json_to_pkl
114 --json '$inputs.db.mpa_pkl' 114 --json '$inputs.db.mpa_pkl'
115 --pkl 'ref_db/custom_db.pkl' 115 --pkl 'ref_db/custom_db.pkl'
121 '$file_path' 121 '$file_path'
122 --input_type '$ext' 122 --input_type '$ext'
123 --read_min_len $inputs.in.read_min_len 123 --read_min_len $inputs.in.read_min_len
124 --bt2_ps '$inputs.in.mapping.bt2_ps' 124 --bt2_ps '$inputs.in.mapping.bt2_ps'
125 --min_mapq_val $inputs.in.mapping.min_mapq_val 125 --min_mapq_val $inputs.in.mapping.min_mapq_val
126 #if $ext == "sam"
127 --nreads \$(cat '$file_path' | grep -c -v '^@')
128 #end if
126 #else 129 #else
127 '$inputs.in.in' 130 '$inputs.in.in'
128 --input_type '$inputs.in.selector' 131 --input_type '$inputs.in.selector'
132 #if $inputs.in.selector == "sam"
133 --nreads \$(cat '$inputs.in.in' | grep -c -v '^@')
134 #end if
129 #end if 135 #end if
130 #if $inputs.db.db_selector == "cached" 136 #if $inputs.db.db_selector == "cached"
131 --bowtie2db '$inputs.db.cached_db.fields.path' 137 --bowtie2db '$inputs.db.cached_db.fields.path'
132 --index '$inputs.db.cached_db.fields.dbkey' 138 --index '$inputs.db.cached_db.fields.dbkey'
133 #else 139 #else
332 <section name="out" title="Outputs" expanded="true"> 338 <section name="out" title="Outputs" expanded="true">
333 <param argument="--sample_id_key" type="text" value="SampleID" label="Sample ID key for this analysis"/> 339 <param argument="--sample_id_key" type="text" value="SampleID" label="Sample ID key for this analysis"/>
334 <param argument="--sample_id" type="text" value="Metaphlan_Analysis" label="Sample ID for this analysis"/> 340 <param argument="--sample_id" type="text" value="Metaphlan_Analysis" label="Sample ID for this analysis"/>
335 <param argument="--use_group_representative" type='boolean' checked="false" truevalue='--use_group_representative' falsevalue='' 341 <param argument="--use_group_representative" type='boolean' checked="false" truevalue='--use_group_representative' falsevalue=''
336 label="Use a species as representative for species groups?"/> 342 label="Use a species as representative for species groups?"/>
337 <param name="legacy_output" argument="--legacy-output" type='boolean' checked="false" truevalue='--legacy-output' falsevalue='' 343 <param argument="--legacy-output" type='boolean' checked="false" truevalue='--legacy-output' falsevalue=''
338 label="Old MetaPhlAn2 two columns output?"/> 344 label="Old MetaPhlAn2 two columns output?"/>
339 <param argument="--CAMI_format_output" type='boolean' checked="false" truevalue='--CAMI_format_output' falsevalue='' 345 <param argument="--CAMI_format_output" type='boolean' checked="false" truevalue='--CAMI_format_output' falsevalue=''
340 label="Report the profiling using the CAMI output format?"/> 346 label="Report the profiling using the CAMI output format?"/>
341 <param argument="--unknown_estimation" type='boolean' checked="false" truevalue='--unknown_estimation' falsevalue='' 347 <param argument="--unknown_estimation" type='boolean' checked="false" truevalue='--unknown_estimation' falsevalue=''
342 label="Scale relative abundances to the number of reads mapping to known clades in order to estimate unknowness?"/> 348 label="Scale relative abundances to the number of reads mapping to known clades in order to estimate unknowness?"/>
406 <param name="unknown_estimation" value="false"/> 412 <param name="unknown_estimation" value="false"/>
407 <param name="krona_output" value="true"/> 413 <param name="krona_output" value="true"/>
408 </section> 414 </section>
409 <output name="output_file" ftype="tabular"> 415 <output name="output_file" ftype="tabular">
410 <assert_contents> 416 <assert_contents>
411 <has_text text="UNKNOWN"/> 417 <has_text text="UNCLASSIFIED"/>
412 </assert_contents> 418 </assert_contents>
413 </output> 419 </output>
414 <output name="bowtie2out" ftype="tabular"> 420 <output name="bowtie2out" ftype="tabular">
415 <assert_contents> 421 <assert_contents>
416 <not_has_text text="HWI-EAS109_102883399:3:104:7342:14360/1"/> 422 <not_has_text text="HWI-EAS109_102883399:3:104:7342:14360/1"/>
501 </element> 507 </element>
502 </output_collection> 508 </output_collection>
503 <output name="krona_output_file" ftype="tabular"> 509 <output name="krona_output_file" ftype="tabular">
504 <assert_contents> 510 <assert_contents>
505 <not_has_text text="k__Bacteria"/> 511 <not_has_text text="k__Bacteria"/>
506 <has_n_lines n="0"/> 512 <has_n_lines n="1" delta="1"/>
513 <has_size value="1" delta="1"/>
507 </assert_contents> 514 </assert_contents>
508 </output> 515 </output>
509 </test> 516 </test>
510 <test expect_num_outputs="6"> 517 <test expect_num_outputs="6">
511 <section name="inputs"> 518 <section name="inputs">
1049 <help><![CDATA[ 1056 <help><![CDATA[
1050 What it does 1057 What it does
1051 ============ 1058 ============
1052 1059
1053 MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, 1060 MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria,
1054 Archaea and Eukaryotes) from metagenomic shotgun sequencing data (i.e. not 16S) with species-level. 1061 Archaea and Eukaryotes) from metagenomic shotgun sequencing data (i.e. not 16S) at species-level.
1055 1062
1056 MetaPhlAn relies on ~1.1M unique clade-specific marker genes identified from ~100,000 reference genomes 1063 MetaPhlAn relies on ~1.1M unique clade-specific marker genes identified from ~100,000 reference genomes
1057 (~99,500 bacterial and archaeal and ~500 eukaryotic), allowing: 1064 (~99,500 bacterial and archaeal and ~500 eukaryotic), allowing:
1058 1065
1059 - unambiguous taxonomic assignments; 1066 - unambiguous taxonomic assignments;
1075 1082
1076 MetaPhlAn introduces the capability of characterizing organisms at the strain level using non 1083 MetaPhlAn introduces the capability of characterizing organisms at the strain level using non
1077 aggregated marker information. Such capability comes with several slightly different flavours and 1084 aggregated marker information. Such capability comes with several slightly different flavours and
1078 are a way to perform strain tracking and comparison across multiple samples. 1085 are a way to perform strain tracking and comparison across multiple samples.
1079 1086
1080 Usually, MetaPhlAn is first ran with the default parameter for the type of analysis to profile the 1087 Usually, MetaPhlAn is first ran with default parameters for the type of analysis to profile the
1081 species present in the community, and then a strain-level profiling can be performed to zoom-in into 1088 species present in the community, and then a strain-level profiling can be performed to zoom-in on
1082 specific species of interest. This operation can be performed quickly as it exploits the bowtie2out 1089 specific species of interest. This operation can be performed quickly as it exploits the bowtie2out
1083 intermediate file saved during the execution of the default analysis type. 1090 intermediate file saved during the execution of the default analysis type.
1084 1091
1085 Inputs 1092 Inputs
1086 ====== 1093 ======
1087 1094
1088 Metaphlan takes as input either: 1095 Metaphlan takes as input either:
1089 1096
1090 - one or several sequence files in Fasta, FastQ (compressed or not) 1097 - one or several sequence files in Fasta, FastQ (whether compressed or not)
1091 - a BowTie2 produced SAM file 1098 - a BowTie2 produced SAM file
1092 - an intermediary mapping file of the microbiota generated by a previous MetaPhlAn run 1099 - an intermediary mapping file of the microbiota generated by a previous MetaPhlAn run
1093 1100
1094 It also need the reference database, which can be locally installed or customized using the dedicated tools. 1101 It also needs the reference database, which can be locally installed or customized using the dedicated tools.
1095 1102
1096 Outputs 1103 Outputs
1097 ======= 1104 =======
1098 1105
1099 The main output file is a tab-separated file with the predicted taxon relative abundances. 1106 The main output is a tab-separated file with the predicted taxon relative abundances.
1100 1107
1101 It also generates a BIOM file and some intermediate files (SAM and BowTie2out) if sequence files are given as inputs. 1108 It also generates a BIOM file and some intermediate files (SAM and BowTie2out) if sequence files are given as inputs.
1102 1109
1103 1110
1104 More help and use cases 1111 More help and use cases
1105 ======================= 1112 =======================
1106 1113
1107 To get more information about MetaPhlAn usage and use cases, please refer to the `Metaphlan documentation`_. 1114 To get more information about MetaPhlAn usage and use cases, please refer to the `Metaphlan documentation`_.
1108 1115
1109 .. _Metaphlan documentation: https://github.com/biobakery/MetaPhlAn/wiki/MetaPhlAn-3.0#basic-usage 1116 .. _Metaphlan documentation: https://github.com/biobakery/MetaPhlAn/wiki/MetaPhlAn-4#Basic-Usage
1110 1117
1111 ]]></help> 1118 ]]></help>
1112 <expand macro="citations"/> 1119 <expand macro="citations"/>
1113 </tool> 1120 </tool>