| Previous changeset 7:d753d9169482 (2021-07-21) Next changeset 9:df7a52791be9 (2024-02-25) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 061757dd7b3bfe66b7738fd54bd6c5e135d9afe8 |
|
modified:
hmmsearch.xml macros.xml |
|
added:
test-data/cut_ga_test.out |
| b |
| diff -r d753d9169482 -r 3bb58751f4ee hmmsearch.xml --- a/hmmsearch.xml Wed Jul 21 14:14:52 2021 +0000 +++ b/hmmsearch.xml Mon Nov 06 20:22:49 2023 +0000 |
| [ |
| @@ -1,9 +1,10 @@ <?xml version="1.0"?> -<tool id="hmmer_hmmsearch" name="hmmsearch" version="@TOOL_VERSION@+galaxy0"> +<tool id="hmmer_hmmsearch" name="hmmsearch" version="@TOOL_VERSION@+galaxy1"> <description>search profile(s) against a sequence database</description> - <macros> + <macros> <import>macros.xml</import> </macros> + <expand macro="bio_tools"/> <expand macro="requirements"/> <expand macro="stdio"/> <command><![CDATA[ @@ -12,7 +13,7 @@ @OFORMAT_WITH_OPTS@ @THRESHOLDS@ -@CUT@ +@THRESHOLDS_DOM@ @ACCEL_HEUR@ @ADV_OPTS@ @CPU@ @@ -27,8 +28,7 @@ <!-- todo use Galaxy features like data libraries/data tables/??? --> <param name="seqdb" type="data" format="fasta" label="Sequence database to search against"/> <expand macro="oformat_with_opts_dom_pfam"/> - <expand macro="thresholds_xml"/> - <expand macro="cut"/> + <expand macro="thresholds_cut_dom_xml"/> <expand macro="accel_heur_xml"/> <expand macro="adv_opts"/> <expand macro="seed"/> @@ -65,6 +65,41 @@ <expand macro="assert_out" tool="hmmsearch"/> </output> </test> + <test expect_num_outputs="1"><!-- test with additional evalue threshold options set --> + <param name="hmmfile" value="fn3.hmm"/> + <param name="seqdb" value="uniprot_matches.fasta"/> + <conditional name="repopt"> + <param name="incE" value="0.00001"/> + <param name="incdomE" value="0.0001"/> + </conditional> + <expand macro="oformat_test" /> + <param name="oformat" value=""/> + <expand macro="seed_test" /> + <output name="output"> + <expand macro="assert_out" tool="hmmsearch"/> + </output> + <assert_command> + <has_text text="-E 10"/> + <has_text text="--incE 1e-05"/> + <has_text text="--domE 10"/> + <has_text text="--incdomE 0.0001"/> + </assert_command> + </test> + <test expect_num_outputs="1"><!-- test with cut_ga set --> + <param name="hmmfile" value="fn3.hmm"/> + <param name="seqdb" value="uniprot_matches.fasta"/> + <conditional name="repopt"> + <param name="repopt_sel" value="--cut_ga"/> + </conditional> + <expand macro="oformat_test" /> + <param name="oformat" value=""/> + <expand macro="seed_test" /> + <output name="output" file="cut_ga_test.out" lines_diff="10"> + <expand macro="assert_out" tool="hmmsearch"/> + </output> + </test> + + </tests> <help><![CDATA[ @HELP_PRE@ |
| b |
| diff -r d753d9169482 -r 3bb58751f4ee macros.xml --- a/macros.xml Wed Jul 21 14:14:52 2021 +0000 +++ b/macros.xml Mon Nov 06 20:22:49 2023 +0000 |
| [ |
| b'@@ -6,6 +6,11 @@\n <yield/>\n </requirements>\n </xml>\n+ <xml name="bio_tools">\n+ <xrefs>\n+ <xref type="bio.tools">hmmer3</xref>\n+ </xrefs>\n+ </xml>\n <token name="@TOOL_VERSION@">3.3.2</token>\n <xml name="stdio">\n <stdio>\n@@ -17,69 +22,135 @@\n <regex match="Exception:"/>\n </stdio>\n </xml>\n+\n+ <!-- command line for thresholds_* -->\n <token name="@THRESHOLDS@">\n--E $E\n---domE $domE\n-\n-#if str($T):\n- -T $T\n-#end if\n-\n-#if str($domT):\n- --domT $domT\n+#if $repopt.repopt_sel == "evalue"\n+ -E $repopt.E\n+ #if str($repopt.incE) != ""\n+ --incE $repopt.incE\n+ #end if\n+#elif $repopt.repopt_sel == "score"\n+ -T $repopt.T\n+ #if str($repopt.incT) != ""\n+ --incT $repopt.incT\n+ #end if\n+#else\n+ $repopt.repopt_sel\n #end if\n-\n-#if str($incE):\n- --incE $incE\n-#end if\n-\n-#if str($incdomE):\n- --incdomE $incdomE\n-#end if\n-\n-#if str($incT):\n- --incT $incT\n-#end if\n-\n-#if str($incdomT):\n- --incdomT $incdomT\n+ </token>\n+ <!-- additional command line thresholds*dom* -->\n+ <token name="@THRESHOLDS_DOM@">\n+#if $repopt.repopt_sel == "evalue"\n+ --domE $repopt.domE\n+ #if str($repopt.incdomE) != ""\n+ --incdomE $repopt.incdomE\n+ #end if\n+#elif $repopt.repopt_sel == "score"\n+ --domT $repopt.domT\n+ #if str($repopt.incdomT) != ""\n+ --incdomT $repopt.incdomT\n+ #end if\n #end if\n </token>\n+\n <xml name="thresholds_xml">\n- <!-- Options controlling reporting thresholds -->\n- <param argument="-E" type="float" min="0" value="10.0" label="report sequences <= this E-Value threshold in output" />\n- <param argument="--domE" type="float" min="0" value="10.0" label="report domains <= this E-Value threshold in output" />\n- <param argument="-T" type="float" optional="true" label="report sequences >= this score threshold in output" />\n- <param argument="--domT" type="float" optional="true" label="report domains >= this score threshold in output" />\n <!-- Options controlling inclusion (significance) thresholds -->\n- <param argument="--incE" type="float" optional="true" label="consider sequences <= this E-Value threshold as significant" />\n+ <conditional name="repopt">\n+ <param name="repopt_sel" type="select" label="Threshold option">\n+ <option value="evalue" selected="true">E-value (reporting threshold)</option>\n+ <option value="score">Score (reporting threshold)</option>\n+ <yield name="additional_options"/>\n+ </param>\n+ <when value="evalue">\n+ <param argument="-E" type="float" min="0" value="10" label="E-value threshold" help="Report sequences <= this E-Value threshold in output. Default: 10.0" />\n+ <param argument="--incE" type="float" optional="true" label="consider sequences <= this E-Value threshold as significant" />\n+ <yield name="edom_params"/>\n+ </when>\n+ <when value="score">\n+ <param argument="-T" type="float" value="" label="Score Threshold" help="Report sequences >= this score threshold in output. This option is incompatible with -E, --cut_ga,--cut_nc" />\n+ <param argument="--incT" type="float" optional="true" label="consider sequences >= this score threshold as significant" />\n+ <yield name="tdom_params"/>\n+ </when>\n+ <yield name="additional_whens"/>\n+ </conditional>\n+ </xml>\n+\n+ <xml name="thresholds_dom_xml">\n+ <expand macro="thresholds_xml">\n+ <token name="edom_params">\n+ <expand macro="dome_thresholds"/>\n+ </token>\n+ <token name="tdom_params">\n+ <expand macro="domt_thresholds"/>\n+ </token>\n+ </expand>\n+ </xml>\n+\n+ <xml name="thresholds_cut_xml">\n+ <expand macro="thresholds_xml">\n+ <token name="additional_options">\n+ <expand macro="model_specific_options"/>\n+ </token>\n+ <token name="additional_whens">\n+ <expand macro="model_specific_whens"/>\n+ </token>\n+ </expand>\n+ </xml>\n+ \n+ <xml name="thresholds_cut_dom_xml">\n+ <expand ma'..b't;= this score threshold in output. This option is incompatible with --domE, --cut_ga" />\n <param argument="--incdomT" type="float" optional="true" label="consider domains >= this score threshold as significant" />\n </xml>\n- <token name="@THRESHOLDS_NODOM@">\n--E $E\n \n-#if str($T):\n- -T $T\n-#end if\n-\n-#if str($incE):\n- --incE $incE\n-#end if\n-\n-#if str($incT):\n- --incT $incT\n-#end if\n- </token>\n <xml name="thresholds_nodom">\n <!-- Options controlling reporting thresholds -->\n- <param argument="-E" type="float" min="0" value="10.0" label="report sequences <= this E-Value threshold in output" />\n- <param argument="-T" type="float" optional="true" label="report sequences >= this score threshold in output" />\n+ <param argument="-E" type="float" min="0" optional="true" label="E-Value Threshold" help="Report sequences <= this E-Value threshold in output. Default: 10.0. This option is incompatible with option -T,--cut_ga, --cut_nc" />\n+ <param argument="-T" type="float" optional="true" label="Score Threshold" help="Report sequences >= this score threshold in output. This option is incompatible with -E, --cut_ga,--cut_nc" />\n <!-- Options controlling inclusion (significance) thresholds -->\n <param argument="--incE" type="float" optional="true" label="consider sequences <= this E-Value threshold as significant" />\n <param argument="--incT" type="float" optional="true" label="consider sequences >= this score threshold as significant" />\n </xml>\n+ <xml name="cut">\n+ <param argument="--cut_ga" type="boolean" truevalue="--cut_ga" falsevalue="" label="use profile\'s GA gathering cutoffs to set all thresholding" help="This option is incompatible with options -E,-T,--domE,--domT" />\n+ <param argument="--cut_nc" type="boolean" truevalue="--cut_nc" falsevalue="" label="use profile\'s NC gathering cutoffs to set all thresholding" help="This option is incompatible with options -E,-T,--domE,--domT" />\n+ <param argument="--cut_tc" type="boolean" truevalue="--cut_tc" falsevalue="" label="use profile\'s TC gathering cutoffs to set all thresholding" />\n+ </xml>\n+\n <token name="@ACCEL_HEUR@">\n $max\n --F1 $F1\n@@ -115,7 +186,7 @@\n <param argument="--Eft" type="float" min="0" max="1" value="0.04" label="tail mass for Forward exponential tail tau fit" />\n </xml>\n <token name="@OFORMAT_WITH_OPTS@">\n-#if $oformat: \n+#if $oformat:\n #for o in str($oformat).split(\',\'):\n --$o \'$getVar($o, \'MISSING_OUTPUT\'+$o)\'\n #end for\n@@ -144,7 +215,7 @@\n <expand macro="oformat_with_opts_dom">\n <option value="pfamtblout" selected="true">Table of hits and domains in Pfam format (--pfamtblout)</option>\n </expand>\n- </xml> \n+ </xml>\n \n <xml name="oformat_with_opts_dfam_alisc">\n <!-- Options directing output -->\n@@ -192,14 +263,14 @@\n <has_line_matching expression="# @TOOL@.*"/>\n <has_line_matching expression="\\[ok\\]"/>\n </assert_contents>\n- </xml> \n+ </xml>\n \n <xml name="assert_tblout" token_tool="">\n <assert_contents>\n <has_line_matching expression="# Program: @TOOL@"/>\n <has_line_matching expression="# \\[ok\\]"/>\n </assert_contents>\n- </xml> \n+ </xml>\n \n <xml name="oformat_test">\n <param name="notextw" value="true" />\n@@ -342,16 +413,6 @@\n </when>\n </conditional>\n </xml>\n- <token name="@CUT@">\n-$cut_ga\n-$cut_nc\n-$cut_tc\n- </token>\n- <xml name="cut">\n- <param argument="--cut_ga" type="boolean" truevalue="--cut_ga" falsevalue="" label="use profile\'s GA gathering cutoffs to set all thresholding" />\n- <param argument="--cut_nc" type="boolean" truevalue="--cut_nc" falsevalue="" label="use profile\'s NC gathering cutoffs to set all thresholding" />\n- <param argument="--cut_tc" type="boolean" truevalue="--cut_tc" falsevalue="" label="use profile\'s TC gathering cutoffs to set all thresholding" />\n- </xml>\n <token name="@MCSS@">\n --$mcs.model_construction_strategy_select\n \n' |
| b |
| diff -r d753d9169482 -r 3bb58751f4ee test-data/cut_ga_test.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cut_ga_test.out Mon Nov 06 20:22:49 2023 +0000 |
| [ |
| @@ -0,0 +1,45 @@ +# hmmsearch :: search profile(s) against a sequence database +# HMMER 3.3.2 (Nov 2020); http://hmmer.org/ +# Copyright (C) 2020 Howard Hughes Medical Institute. +# Freely distributed under the BSD open source license. +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - +# query HMM file: /tmp/saskia/tmpug0qcpsy/files/9/9/b/dataset_99bcd3c6-6d16-4e09-9878-7117f928bb24.dat +# target sequence database: /tmp/saskia/tmpug0qcpsy/files/f/9/9/dataset_f99d0a82-fcb5-4323-b2d4-8b218045c72e.dat +# max ASCII text line length: unlimited +# model-specific thresholding: GA cutoffs +# Vit filter P threshold: <= 0.001 +# Fwd filter P threshold: <= 1e-05 +# random number seed set to: 4 +# number of worker threads: 0 +# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + +Query: fn3 [M=86] +Accession: PF00041.13 +Description: Fibronectin type III domain +Scores for complete sequences (score includes all domains): + --- full sequence --- --- best 1 domain --- -#dom- + E-value score bias E-value score bias exp N Sequence Description + ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- + + [No hits detected that satisfy reporting thresholds] + + +Domain annotation for each sequence (and alignments): + + [No targets detected that satisfy reporting thresholds] + + +Internal pipeline statistics summary: +------------------------------------- +Query model(s): 1 (86 nodes) +Target sequences: 2 (301 residues searched) +Passed MSV filter: 0 (0); expected 0.0 (0.02) +Passed bias filter: 0 (0); expected 0.0 (0.02) +Passed Vit filter: 0 (0); expected 0.0 (0.001) +Passed Fwd filter: 0 (0); expected 0.0 (1e-05) +Initial search space (Z): 2 [actual number of targets] +Domain search space (domZ): 0 [number of targets reported over threshold] +# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 +# Mc/sec: 144.45 +// +[ok] |