Mercurial > repos > oinizan > frogs
diff frogsfunc_functions.xml @ 22:57824202c333 draft
planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 2472c451b3e27c98ce60b2e56a78fd3fbe0fb2d6-dirty
| author | oinizan |
|---|---|
| date | Mon, 22 May 2023 08:02:36 +0000 |
| parents | 74a9b83110a7 |
| children | dfaf556d2a20 |
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--- a/frogsfunc_functions.xml Thu Mar 30 06:09:01 2023 +0000 +++ b/frogsfunc_functions.xml Mon May 22 08:02:36 2023 +0000 @@ -16,7 +16,7 @@ # along with this program. If not, see <http://www.gnu.org/licenses/>. --> <tool id="FROGSFUNC_step3_functions" name="FROGSFUNC_2_functions" version= "@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> - <description>Calculates functions abundances in each sample.</description> + <description>Calculates functions abundances in each sample. </description> <macros> <import>macros.xml</import> @@ -95,12 +95,12 @@ </inputs> <outputs> <data format="html" name="summary_file" label="${tool.name}: report.html" from_work_dir="report.html"/> - <data format="biom1" name="output_biom" label="${tool.name}: frogsfunc_functions.biom" from_work_dir="frogsfunc_functions.biom"/> - <data format="fasta" name="output_fasta" label="${tool.name}: frogsfunc_functions.fasta" from_work_dir="frogsfunc_functions.fasta"/> + <data format="biom1" name="output_biom" label="${tool.name}: frogsfunc_functions_asv_abundances.biom" from_work_dir="frogsfunc_functions.biom"/> + <data format="fasta" name="output_fasta" label="${tool.name}: frogsfunc_functions_asv.fasta" from_work_dir="frogsfunc_functions.fasta"/> <data format="tsv" name="output_otu_norm" label="${tool.name}: frogsfunc_functions_marker_norm.tsv" from_work_dir="frogsfunc_functions_marker_norm.tsv.tsv"/> <data format="tsv" name="output_weighted" label="${tool.name}: frogsfunc_functions_weighted_nsti.tsv" from_work_dir="frogsfunc_functions_weighted_nsti.tsv"/> - <data format="tsv" name="output_excluded" label="${tool.name}: frogsfunc_functions_excluded.tsv" from_work_dir="frogsfunc_functions_excluded.tsv"/> + <data format="tsv" name="output_excluded" label="${tool.name}: frogsfunc_functions_asv_excluded.tsv" from_work_dir="frogsfunc_functions_excluded.tsv"/> <data format="tsv" name="output_copy_ec_abund" label="${tool.name}: EC_copynumbers_predicted.tsv" from_work_dir="EC_copynumbers_predicted.tsv"> <filter>"EC" in functions</filter> </data> @@ -142,15 +142,15 @@ <tests> <test> + <param name="input_fasta" value="references/25-frogsfunc_placeseqs.fasta" /> <param name="input_biom" value="references/25-frogsfunc_placeseqs.biom" /> - <param name="function" value="references/26-frogsfunc_copynumbers_predicted_functions.tsv" /> - <param name="marker" value="references/26-frogsfunc_copynumbers_marker.tsv"/> + <param name="input_tree" value="references/25-frogsfunc_placeseqs_tree.nwk" /> + <param name="input_marker" value="references/25-frogsfunc_copynumbers_marker.tsv" /> + <param name="category.value" value="frogs_picrust2_marker_table" /> + <param name="functions" value="EC" /> <param name="max_nsti" value="2" /> - <param name="min_reads" value="1" /> - <param name="min_samples" value="1" /> - <param name="strat" value="false" /> - <output name="output_function_abund" file="references/27-frogsfunc_functions_unstrat.tsv" compare="diff" lines_diff="0" /> + <output name="output_function_ec_abund" file="references/27-frogsfunc_functions_unstrat.tsv" compare="diff" lines_diff="0" /> <output name="output_otu_norm" file="references/27-frogsfunc_functions_marker_norm.tsv" compare="diff" lines_diff="0" /> <output name="output_weighted" file="references/27-frogsfunc_functions_weighted_nsti.tsv" compare="diff" lines_diff="0" /> <output name="summary_file" file="references/27-frogsfunc_functions_report.html" compare="diff" lines_diff="0" /> @@ -255,7 +255,7 @@ Sequence file without excluded ASVs (NSTI, blast perc identity or blast perc coverage thresholds). (FROGSFUNC_2_functions.fasta) -**-ASV abundance Biom file - one per chosen target function database (EC, KO, PFAM, COG, TIGRFAM,PHENO)-**: +**-ASV abundance Biom file-**: ASV abundance data i a biom file without excluded ASVs (NSTI, %identity or %coverage thresholds alignment). (FROGSFUNC_2_functions.biom)