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comparison humann.xml @ 2:2cd76b089570 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 0966faf8782e9043772acfa32f4a4281687a19dd
author iuc
date Tue, 07 Feb 2023 19:47:50 +0000
parents 6b7622dda516
children 037c0b25c041
comparison
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1:6b7622dda516 2:2cd76b089570
16 </options> 16 </options>
17 </param> 17 </param>
18 </when> 18 </when>
19 <when value="history"> 19 <when value="history">
20 <param argument="--bowtie2db" type="data" format="fasta" label="Database with clade-specific marker genes from history"/> 20 <param argument="--bowtie2db" type="data" format="fasta" label="Database with clade-specific marker genes from history"/>
21 <param argument="--mpa_pkl" type="data" format="json" label="Metadata associate to the database with clade-specific marker genes from history"/> 21 <param argument="--mpa_pkl" type="data" format="json" label="Metadata associated to the database with clade-specific marker genes from history"/>
22 </when> 22 </when>
23 </conditional> 23 </conditional>
24 <param argument="--prescreen-threshold" type="float" value="0.01" min="0" max="100" label="Minimum percentage of reads matching a species"/> 24 <param argument="--prescreen-threshold" type="float" value="0.01" min="0" max="100" label="Minimum percentage of reads matching a species"/>
25 <!-- add metaphlan options --> 25 <!-- add metaphlan options -->
26 </section> 26 </section>
27 </xml> 27 </xml>
28 <token name="@PRESCREEN_PREPARE@"><![CDATA[ 28 <token name="@PRESCREEN_PREPARE@"><![CDATA[
29 #if $wf.prescreen.metaphlan_db.selector == "history" 29 #if $wf.prescreen.metaphlan_db.selector == "history"
30 mkdir metaphlan_db 30 mkdir metaphlan_db
31 && 31 &&
32 bowtie2-build '$wf.prescreen.metaphlan_db.bowtie2db' 'metaphlan_db/custom_db-v30' 32 bowtie2-build --large-index '$wf.prescreen.metaphlan_db.bowtie2db' 'metaphlan_db/custom_db-v30'
33 && 33 &&
34 python '$__tool_directory__/customizemetadata.py' 34 python '$__tool_directory__/customizemetadata.py'
35 transform_json_to_pkl 35 transform_json_to_pkl
36 --json '$wf.prescreen.metaphlan_db.mpa_pkl' 36 --json '$wf.prescreen.metaphlan_db.mpa_pkl'
37 --pkl 'metaphlan_db/custom_db-v30.pkl' 37 --pkl 'metaphlan_db/custom_db-v30.pkl'
83 <token name="@NUCLEOTIDE_SEARCH_PREPARE@"><![CDATA[ 83 <token name="@NUCLEOTIDE_SEARCH_PREPARE@"><![CDATA[
84 #if $wf.nucleotide_search.nucleotide_db.selector == 'history' 84 #if $wf.nucleotide_search.nucleotide_db.selector == 'history'
85 mkdir nucleotide_db 85 mkdir nucleotide_db
86 && 86 &&
87 #for $f in $wf.nucleotide_search.nucleotide_db.nucleotide_database: 87 #for $f in $wf.nucleotide_search.nucleotide_db.nucleotide_database:
88 ln -s '$f' 'nucleotide_db/${re.sub('[^\w\-_.]', '_', f.element_identifier)}.v296_201901b' && 88 ln -s '$f' 'nucleotide_db/${re.sub('[^\w\-_.]', '_', f.element_identifier)}.v201901_v31' &&
89 #end for 89 #end for
90 #end if 90 #end if
91 ]]></token> 91 ]]></token>
92 <token name="@NUCLEOTIDE_SEARCH_RUN@"><![CDATA[ 92 <token name="@NUCLEOTIDE_SEARCH_RUN@"><![CDATA[
93 #if $wf.nucleotide_search.nucleotide_db.selector == 'history' 93 #if $wf.nucleotide_search.nucleotide_db.selector == 'history'
391 <data format="fasta" name="diamond_unaligned" from_work_dir="output/*_temp/*_diamond_unaligned.fa" label="${tool.name} on ${on_string}: Translated alignment unaligned reads" > 391 <data format="fasta" name="diamond_unaligned" from_work_dir="output/*_temp/*_diamond_unaligned.fa" label="${tool.name} on ${on_string}: Translated alignment unaligned reads" >
392 <filter>out['intermediate_temp'] and "diamond_unaligned" in out['intermediate_temp']</filter> 392 <filter>out['intermediate_temp'] and "diamond_unaligned" in out['intermediate_temp']</filter>
393 </data> 393 </data>
394 </outputs> 394 </outputs>
395 <tests> 395 <tests>
396 <!-- This test refers to the Metaphlan v3 DB format, and hence should fail, which is to be caught gracefully. -->
397 <test expect_exit_code="42" expect_failure="true">
398 <conditional name="in">
399 <!-- raw fasta file -->
400 <param name="selector" value="raw"/>
401 <param name="input" value="demo.fastq.gz"/>
402 </conditional>
403 <conditional name="wf">
404 <!-- full workflow -->
405 <param name="selector" value="none"/>
406 <section name="prescreen">
407 <conditional name="metaphlan_db">
408 <param name="selector" value="history"/>
409 <param name="bowtie2db" value="test-db/metaphlan-db/demo-db-v30.fasta"/>
410 <param name="mpa_pkl" value="test-db/metaphlan-db/old-structure/demo-db-v30.json"/>
411 </conditional>
412 <param name="prescreen_threshold" value="0.01"/>
413 </section>
414 <section name="nucleotide_search">
415 <conditional name="nucleotide_db">
416 <param name="selector" value="history"/>
417 <param name="nucleotide_database">
418 <collection type="list">
419 <element name="g__Bacteroides.s__Bacteroides_stercoris.centroids" ftype="fasta.gz" value="test-db/nucleotide-db/g__Bacteroides.s__Bacteroides_dorei.centroids.v201901_v31.ffn.gz" />
420 <element name="g__Bacteroides.s__Bacteroides_vulgatus.centroids" ftype="fasta.gz" value="test-db/nucleotide-db/g__Bacteroides.s__Bacteroides_vulgatus.centroids.v201901_v31.ffn.gz" />
421 </collection>
422 </param>
423 </conditional>
424 </section>
425 </conditional>
426 </test>
427 <!-- This test refers to the Metaphlan v4 DB format, and hence should be a straight pass. -->
396 <test expect_num_outputs="12"> 428 <test expect_num_outputs="12">
397 <conditional name="in"> 429 <conditional name="in">
398 <!-- raw fasta file --> 430 <!-- raw fasta file -->
399 <param name="selector" value="raw"/> 431 <param name="selector" value="raw"/>
400 <param name="input" value="demo.fastq.gz"/> 432 <param name="input" value="demo.fastq.gz"/>
413 <section name="nucleotide_search"> 445 <section name="nucleotide_search">
414 <conditional name="nucleotide_db"> 446 <conditional name="nucleotide_db">
415 <param name="selector" value="history"/> 447 <param name="selector" value="history"/>
416 <param name="nucleotide_database"> 448 <param name="nucleotide_database">
417 <collection type="list"> 449 <collection type="list">
418 <element name="g__Bacteroides.s__Bacteroides_stercoris.centroids" ftype="fasta.gz" value="test-db/nucleotide-db/g__Bacteroides.s__Bacteroides_dorei.centroids.v296_201901b.ffn.gz" /> 450 <element name="g__Bacteroides.s__Bacteroides_stercoris.centroids" ftype="fasta.gz" value="test-db/nucleotide-db/g__Bacteroides.s__Bacteroides_dorei.centroids.v201901_v31.ffn.gz"/>
419 <element name="g__Bacteroides.s__Bacteroides_vulgatus.centroids" ftype="fasta.gz" value="test-db/nucleotide-db/g__Bacteroides.s__Bacteroides_vulgatus.centroids.v296_201901b.ffn.gz" /> 451 <element name="g__Bacteroides.s__Bacteroides_vulgatus.centroids" ftype="fasta.gz" value="test-db/nucleotide-db/g__Bacteroides.s__Bacteroides_vulgatus.centroids.v201901_v31.ffn.gz"/>
420 </collection> 452 </collection>
421 </param> 453 </param>
422 </conditional> 454 </conditional>
423 <param name="nucleotide_identity_threshold" value="0"/> 455 <param name="nucleotide_identity_threshold" value="0"/>
424 <param name="nucleotide_subject_coverage_threshold" value="50"/> 456 <param name="nucleotide_subject_coverage_threshold" value="50"/>
919 <has_text text="Total gene families from nucleotide alignment: 545"/> 951 <has_text text="Total gene families from nucleotide alignment: 545"/>
920 <has_text text="Bypass translated search"/> 952 <has_text text="Bypass translated search"/>
921 </assert_contents> 953 </assert_contents>
922 </output> 954 </output>
923 </test> 955 </test>
956 <!-- This test should fail for as metaphlan v4 is invoked on outdated input DB. -->
957 <test expect_exit_code="1" expect_failure="true">
958 <conditional name="in">
959 <!-- raw fasta file -->
960 <param name="selector" value="raw"/>
961 <param name="input" value="demo.fastq.gz"/>
962 </conditional>
963 <conditional name="wf">
964 <!-- bypass_translated_search -->
965 <param name="selector" value="bypass_translated_search"/>
966 <section name="prescreen">
967 <conditional name="metaphlan_db">
968 <param name="selector" value="cached"/>
969 <param name="cached_db" value="metaphlan-db-old-structure"/>
970 </conditional>
971 </section>
972 <section name="nucleotide_search">
973 <conditional name="nucleotide_db">
974 <param name="selector" value="cached"/>
975 <param name="nucleotide_database" value="chocophlan-DEMO-20210421"/>
976 </conditional>
977 </section>
978 </conditional>
979 </test>
924 </tests> 980 </tests>
925 <help><![CDATA[ 981 <help><![CDATA[
926 @HELP_HEADER@ 982 @HELP_HEADER@
927 983
928 This tool corresponds to the main tool in HUMAnN pipeline: 984 This tool corresponds to the main tool in HUMAnN pipeline:
973 1029
974 - Pre-computed (typically gene) abundance tables 1030 - Pre-computed (typically gene) abundance tables
975 1031
976 1032
977 HUMAnN uses 3 reference databases 1033 HUMAnN uses 3 reference databases
978 Locally cached databases have to be downloaded database before using them (using the dedicated tool). Custom databases can also be used after upload. 1034 Locally cached databases have to be downloaded before using them (using the dedicated tool). Custom databases can also be used after upload.
979 1035
980 Outputs 1036 Outputs
981 ======= 1037 =======
982 1038
983 HUMAnN creates three output files: 1039 HUMAnN creates three output files: