| Previous changeset 7:ab12df91b47f (2020-11-05) Next changeset 9:00dd059b77e5 (2020-12-08) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit f20b079c868afb2decc111751312b7f2a43f1dfd" |
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modified:
make.contigs.xml |
| b |
| diff -r ab12df91b47f -r 829bb93d3add make.contigs.xml --- a/make.contigs.xml Thu Nov 05 21:48:20 2020 +0000 +++ b/make.contigs.xml Thu Nov 26 04:39:59 2020 +0000 |
| b |
| @@ -1,4 +1,4 @@ -<tool profile="16.07" id="mothur_make_contigs" name="Make.contigs" version="@WRAPPER_VERSION@.0"> +<tool profile="16.07" id="mothur_make_contigs" name="Make.contigs" version="@WRAPPER_VERSION@.1"> <description>Aligns paired forward and reverse fastq files to contigs as fasta and quality</description> <macros> <import>macros.xml</import> @@ -54,7 +54,7 @@ mismatch=$mismatch, gapopen=$gapopen, gapextend=$gapextend, - rename=$rename + rename=$rename, processors='\${GALAXY_SLOTS:-8}' )' | sed 's/ //g' ## mothur trips over whitespace @@ -132,6 +132,7 @@ <output name="qual" file="Mock_S280_L001_R1_001_small.trim.contigs.qual" ftype="qual"/> <output name="report" file="Mock_S280_L001_R1_001_small.contigs.report" ftype="txt"/> <param name="savelog" value="true"/> + <param name="rename" value="false"/> <expand macro="logfile-test"/> </test> <!-- Test with a simple paired collection as input --> @@ -149,6 +150,7 @@ <output name="qual" file="Mock_S280_L001_R1_001_small.trim.contigs.qual" ftype="qual"/> <output name="report" file="Mock_S280_L001_R1_001_small.contigs.report" ftype="txt"/> <param name="savelog" value="true"/> + <param name="rename" value="false"/> <expand macro="logfile-test"/> </test> <!-- Test with a simple paired collection as input + extra parameters specified --> @@ -167,10 +169,53 @@ <param name="mismatch" value="-2"/> <param name="gapopen" value="-3"/> <param name="gapextend" value="-2"/> - <output name="fasta" md5="48e32c65bd9f064c5c0b4ea7695cabe9" ftype="fasta"/> - <output name="qual" md5="1e7778cee0d86bfa2759a07bb4356165" ftype="qual"/> - <output name="report" md5="5274725ef45890fd6da4650d5d536173" ftype="txt"/> + <output name="fasta" md5="48e32c65bd9f064c5c0b4ea7695cabe9" ftype="fasta"> + <assert_contents> + <has_text text=">M00967_43_000000000-A3JHG_1_1101_19936_3208" /> + </assert_contents> + </output> + <output name="qual" md5="1e7778cee0d86bfa2759a07bb4356165" ftype="qual"> + <assert_contents> + <has_text text=">M00967_43_000000000-A3JHG_1_1101_19936_3208" /> + </assert_contents> + </output> + <output name="report" md5="5274725ef45890fd6da4650d5d536173" ftype="txt"> + <assert_contents> + <has_line line="M00967_43_000000000-A3JHG_1_1101_19936_3208	253	249	2	251	0	0" /> + </assert_contents> + </output> <param name="savelog" value="true"/> + <param name="rename" value="false"/> + <expand macro="logfile-test"/> + </test> + <!-- Test with a simple paired collection as input + rename sequences --> + <test> + <conditional name="input_type"> + <param name="type" value="simple_collection"/> + <param name="paired_collection"> + <collection type="paired"> + <element name="forward" value="Mock_S280_L001_R1_001_small.fastq" /> + <element name="reverse" value="Mock_S280_L001_R2_001_small.fastq" /> + </collection> + </param> + </conditional> + <output name="fasta" md5="addcc2f4233df75ab9e5feacadb6850f" ftype="fasta"> + <assert_contents> + <has_text text=">1" /> + </assert_contents> + </output> + <output name="qual" md5="476932c0236a672c0c99cada2b114fe7" ftype="qual"> + <assert_contents> + <has_text text=">1" /> + </assert_contents> + </output> + <output name="report" md5="7634bcab8db8907f80087da03259012a" ftype="txt"> + <assert_contents> + <has_line line="1	253	249	2	251	0	0" /> + </assert_contents> + </output> + <param name="savelog" value="true"/> + <param name="rename" value="true"/> <expand macro="logfile-test"/> </test> <!-- Test with a list:paired collection as input --> @@ -199,6 +244,7 @@ <output name="report" md5="96a07f664105e4ddcb645c7cd9f5d692" ftype="txt"/> <output name="group" md5="ef83b393be4103f0b61a021234905210" ftype="mothur.groups"/> <param name="savelog" value="true"/> + <param name="rename" value="false"/> <expand macro="logfile-test"/> </test> </tests> |