Mercurial > repos > iuc > hmmer_nhmmer
comparison nhmmer.xml @ 5:b4fe2f703b4b draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
| author | iuc |
|---|---|
| date | Tue, 16 Jun 2020 05:38:43 -0400 |
| parents | c8e81e43bff1 |
| children | 314b778b8ffa |
comparison
equal
deleted
inserted
replaced
| 4:be0cc39776f9 | 5:b4fe2f703b4b |
|---|---|
| 7 <expand macro="requirements"/> | 7 <expand macro="requirements"/> |
| 8 <expand macro="stdio"/> | 8 <expand macro="stdio"/> |
| 9 <command><![CDATA[ | 9 <command><![CDATA[ |
| 10 nhmmer | 10 nhmmer |
| 11 | 11 |
| 12 @OFORMAT_WITH_OPTS_N@ | 12 @OFORMAT_WITH_OPTS@ |
| 13 @HSSI@ | 13 @HSSI@ |
| 14 @THRESHOLDS_NODOM@ | 14 @THRESHOLDS_NODOM@ |
| 15 @CUT@ | 15 @CUT@ |
| 16 @ACCEL_HEUR@ | 16 @ACCEL_HEUR@ |
| 17 @FORMAT_SELECTOR@ | 17 @FORMAT_SELECTOR@ |
| 25 > '$output' | 25 > '$output' |
| 26 ]]></command> | 26 ]]></command> |
| 27 <inputs> | 27 <inputs> |
| 28 <expand macro="input_hmm" /> | 28 <expand macro="input_hmm" /> |
| 29 <param name="seqfile" type="data" format="fasta" label="Target sequence file"/> | 29 <param name="seqfile" type="data" format="fasta" label="Target sequence file"/> |
| 30 <expand macro="oformat_with_opts_n"/> | 30 <expand macro="oformat_with_opts_dfam_alisc"/> |
| 31 <expand macro="hssi"/> | 31 <expand macro="hssi"/> |
| 32 <expand macro="thresholds_nodom"/> | 32 <expand macro="thresholds_nodom"/> |
| 33 <expand macro="cut" /> | 33 <expand macro="cut" /> |
| 34 <expand macro="accel_heur_xml"/> | 34 <expand macro="accel_heur_xml"/> |
| 35 <expand macro="format_selector_noprot"/> | 35 <expand macro="format_selector_noprot"/> |
| 37 <expand macro="lengths"/> | 37 <expand macro="lengths"/> |
| 38 <!-- TODO: block_length toponly bottomonly --> | 38 <!-- TODO: block_length toponly bottomonly --> |
| 39 <expand macro="seed"/> | 39 <expand macro="seed"/> |
| 40 </inputs> | 40 </inputs> |
| 41 <outputs> | 41 <outputs> |
| 42 <data format="txt" name="output" label="NHMMER search of $seqfile.name in $hmmfile.name"/> | 42 <expand macro="output_dfam_alisc" tool="NHMMER"/> |
| 43 | |
| 44 <data format="txt" name="tblout" label="Table of per-sequence hits from HMM matches of $seqfile.name in $hmmfile.name"> | |
| 45 <filter>oformat and 'tblout' in oformat</filter> | |
| 46 </data> | |
| 47 <data format="txt" name="dfamtblout" label="Table of per-sequence/per-domain hits from HMM matches of $seqfile.name in $hmmfile.name"> | |
| 48 <filter>oformat and 'pfamtblout' in oformat</filter> | |
| 49 </data> | |
| 50 <data format="txt" name="aliscoresout" label="Scores for positional matches of $seqfile.name in $hmmfile.name"> | |
| 51 <filter>oformat and 'aliscoresout' in oformat</filter> | |
| 52 </data> | |
| 53 </outputs> | 43 </outputs> |
| 54 <tests> | 44 <tests> |
| 55 <test> | 45 <test expect_num_outputs="4"> |
| 56 <param name="hmmfile" value="MADE1.hmm"/> | 46 <param name="hmmfile" value="MADE1.hmm"/> |
| 57 <param name="seqfile" value="dna_target.fa"/> | 47 <param name="seqfile" value="dna_target.fa"/> |
| 58 <expand macro="oformat_test" /> | 48 <expand macro="oformat_test" /> |
| 49 <param name="oformat" value="tblout,dfamtblout,aliscoresout"/> | |
| 59 <expand macro="seed_test" /> | 50 <expand macro="seed_test" /> |
| 60 <output name="output" file="nhmmer.out" lines_diff="10" /> | 51 <output name="output" file="nhmmer.out" lines_diff="16"> |
| 61 <output name="tblout" file="nhmmer.out.tblout" lines_diff="10" /> | 52 <expand macro="assert_out" tool="nhmmer"/> |
| 62 <output name="dfamtblout" file="nhmmer.out.dfamtblout" lines_diff="10" /> | 53 </output> |
| 54 <output name="tblout" file="nhmmer.out.tblout" lines_diff="12"> | |
| 55 <expand macro="assert_tblout" tool="nhmmer"/> | |
| 56 </output> | |
| 57 <output name="aliscoresout" file="nhmmer.out.aliscoresout" lines_diff="10"/> | |
| 58 <output name="dfamtblout" file="nhmmer.out.dfamtblout" lines_diff="10"> | |
| 59 <assert_contents> | |
| 60 <has_line_matching expression="# hit scores"/> | |
| 61 </assert_contents> | |
| 62 </output> | |
| 63 </test> | |
| 64 <test expect_num_outputs="1"> | |
| 65 <param name="hmmfile" value="MADE1.hmm"/> | |
| 66 <param name="seqfile" value="dna_target.fa"/> | |
| 67 <expand macro="oformat_test" /> | |
| 68 <param name="oformat" value=""/> | |
| 69 <expand macro="seed_test" /> | |
| 70 <output name="output" file="nhmmer.out" lines_diff="16"> | |
| 71 <expand macro="assert_out" tool="nhmmer"/> | |
| 72 </output> | |
| 63 </test> | 73 </test> |
| 64 </tests> | 74 </tests> |
| 65 <help><![CDATA[ | 75 <help><![CDATA[ |
| 66 @HELP_PRE@ | 76 @HELP_PRE@ |
| 67 | 77 |