Mercurial > repos > iuc > mapseq
changeset 2:30e275ed0442 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mapseq commit 3652500c9a0b6d92f6dc254cea7dcfcc6522d842
| author | iuc |
|---|---|
| date | Mon, 14 Oct 2024 12:28:09 +0000 |
| parents | f1d1dafc836d |
| children | |
| files | mapseq.xml test-data/sequences.mapseq |
| diffstat | 2 files changed, 33 insertions(+), 3 deletions(-) [+] |
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--- a/mapseq.xml Tue Mar 12 21:22:41 2024 +0000 +++ b/mapseq.xml Mon Oct 14 12:28:09 2024 +0000 @@ -1,7 +1,7 @@ <tool id="mapseq" name="MAPseq" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> <description>sequence read classification designed to assign taxonomy and OTU classifications</description> <macros> - <token name="@TOOL_VERSION@">2.1.1</token> + <token name="@TOOL_VERSION@">2.1.1b</token> <token name="@VERSION_SUFFIX@">0</token> </macros> <xrefs> @@ -38,9 +38,11 @@ ln -s '${ref_db.mscluster}' db.fasta.mscluster && ln -s '${ref_db.mapseq2biom.otu_table}' db.otu && #end if - mapseq -nthreads \${GALAXY_SLOTS:-8} + #if str($seed) != "" + -seed '$seed' + #end if -tophits '$tophits' -topotus '$topotus' -minscore '$minscore' @@ -107,6 +109,8 @@ </when> </conditional> + <param argument="-seed" type="integer" label="Fix random seed" help="Sets a fixed integer seed value for random number generation, ensuring reproducible results" optional="true"/> + <param argument="-tophits" type="integer" label="Top hits" help="Number of reference sequences to include in alignment phase" value="20" min="1" max="200" /> @@ -154,6 +158,9 @@ <param name="mscluster" value="mapseq_db/LSU_trimmed.fasta.mscluster"/> <param name="mapseq2biom" value="no"/> <output name="classifications" file="sequences.mapseq" sort="true"/> + <assert_command> + <has_text text="-seed" negate="true" /> + </assert_command> </test> <test expect_num_outputs="1"> <param name="db_source" value="history" /> @@ -162,6 +169,9 @@ <param name="taxonomy" value="mapseq_db/slv_lsu_filtered2_trimmed.txt"/> <param name="mapseq2biom" value="no"/> <output name="classifications" file="sequences.mapseq" sort="true"/> + <assert_command> + <has_text text="-seed" negate="true" /> + </assert_command> </test> <test expect_num_outputs="3"> <param name="db_source" value="history" /> @@ -172,9 +182,13 @@ <param name="mapseq2biom" value="yes"/> <param name="krona_input" value="no"/> <param name="otu_table" value="mapseq_db/test.otu" /> + <param name="seed" value="12" /> <output name="classifications" file="sequences.mapseq" sort="true"/> <output name="otu_tsv" file="mapseq2biom/tab-output_including_taxIDs.tabular" /> <output name="otu_tsv_notaxid" file="mapseq2biom/tab-output_without_taxIDs.tabular" /> + <assert_command> + <has_text text="-seed '12'" n="1" /> + </assert_command> </test> <test expect_num_outputs="4"> <param name="db_source" value="history" /> @@ -189,6 +203,9 @@ <output name="otu_tsv" file="mapseq2biom/tab-output_including_taxIDs.tabular" /> <output name="otu_tsv_notaxid" file="mapseq2biom/tab-output_without_taxIDs.tabular" /> <output name="krona_format" file="mapseq2biom/krona_input.tabular" /> + <assert_command> + <has_text text="-seed" negate="true" /> + </assert_command> </test> <test expect_num_outputs="1"> <param name="db_source" value="cached" /> @@ -196,6 +213,9 @@ <param name="sequences" value="sequences.fasta"/> <param name="mapseq2biom" value="no"/> <output name="classifications" file="sequences.mapseq" sort="true"/> + <assert_command> + <has_text text="-seed" negate="true" /> + </assert_command> </test> <test expect_num_outputs="3"> <param name="db_source" value="cached" /> @@ -206,6 +226,9 @@ <output name="classifications" file="sequences.mapseq" sort="true"/> <output name="otu_tsv" file="mapseq2biom/tab-output_including_taxIDs.tabular" /> <output name="otu_tsv_notaxid" file="mapseq2biom/tab-output_without_taxIDs.tabular" /> + <assert_command> + <has_text text="-seed" negate="true" /> + </assert_command> </test> <test expect_num_outputs="4"> <param name="db_source" value="cached" /> @@ -213,10 +236,14 @@ <param name="sequences" value="sequences.fasta"/> <param name="mapseq2biom" value="yes"/> <param name="krona_input" value="yes"/> + <param name="seed" value="12" /> <output name="classifications" file="sequences.mapseq" sort="true"/> <output name="otu_tsv" file="mapseq2biom/tab-output_including_taxIDs.tabular" /> <output name="otu_tsv_notaxid" file="mapseq2biom/tab-output_without_taxIDs.tabular" /> <output name="krona_format" file="mapseq2biom/krona_input.tabular" /> + <assert_command> + <has_text text="-seed '12'" n="1" /> + </assert_command> </test> </tests> @@ -289,6 +316,10 @@ ------- * `Apache-2.0 license <https://raw.githubusercontent.com/EBI-Metagenomics/pipeline-v5/master/LICENSE>`_ ]]></help> + <creator> + <person givenName="Rand" familyName="Zoabi" url="https://github.com/RZ9082"/> + <person givenName="Paul" familyName="Zierep" url="https://github.com/paulzierep"/> + </creator> <citations> <citation type="doi"> 10.1093/bioinformatics/btx517
--- a/test-data/sequences.mapseq Tue Mar 12 21:22:41 2024 +0000 +++ b/test-data/sequences.mapseq Mon Oct 14 12:28:09 2024 +0000 @@ -1,4 +1,3 @@ -# mapseq v1.2.6 (Jan 20 2023) #query dbhit bitscore identity matches mismatches gaps query_start query_end dbhit_start dbhit_end strand taxonomy.txt ERR2407324.4-10333.Pue.782.huma-3-1 CP011466.3186026.3188977 48 0.698630154132843 102 41 3 0 146 1156 1299 - sk__Eukaryota;k__Fungi;p__Ascomycota;c__Saccharomycetes;o__Saccharomycetales;f__;g__;s__ ERR2407324.6-10333.Pue.782.huma-5-1 CP011466.3186026.3188977 82 0.8026315569877625 122 28 2 0 150 1147 1299 - sk__Eukaryota;k__Fungi;p__Ascomycota;c__Saccharomycetes;o__Saccharomycetales;f__;g__;s__