Mercurial > repos > iuc > merge_metaphlan_tables

changeset 12:7f5d7b0e9884 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 70ba929dd55348ee43753e6ae29bd45c5cdf5471
author iuc
date Sat, 10 Feb 2024 23:56:53 +0000
parents 0270541aaf46
children 327d9f4cc95f
files macros.xml merge_metaphlan_tables.xml test-data/SRS014464-Anterior_nares-abundances-samefiledifferentname.tabular
diffstat 3 files changed, 42 insertions(+), 6 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Thu Apr 20 11:26:31 2023 +0000
+++ b/macros.xml	Sat Feb 10 23:56:53 2024 +0000
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <macros>
     <token name="@TOOL_VERSION@">4.0.6</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@VERSION_SUFFIX@">2</token>
     <token name="@PROFILE@">22.05</token>
     <!-- Metaphlan DB compatible with this version of Metaphlan
     v4 introduced single genome level bins (SGB) and the index syntax differs from previous versions --> 
--- a/merge_metaphlan_tables.xml	Thu Apr 20 11:26:31 2023 +0000
+++ b/merge_metaphlan_tables.xml	Sat Feb 10 23:56:53 2024 +0000
@@ -7,9 +7,13 @@
     <expand macro="requirements"/>
     <version_command>metaphlan -v</version_command>
     <command detect_errors="aggressive"><![CDATA[
-merge_metaphlan_tables.py
-    #for $element in $inputs
-        '$element'
+    #for $input in $inputs
+        ln -s '$input' '${input.element_identifier}' &&
+    #end for
+
+    merge_metaphlan_tables.py
+    #for $input in $inputs
+        '${input.element_identifier}'
     #end for
     > '$output'
 ]]>
@@ -22,11 +26,12 @@
     </outputs>
     <tests>
         <test expect_num_outputs="1">
-            <param name="inputs" value="SRS014464-Anterior_nares-abundances.tabular,SRS014464-Anterior_nares-abundances.tabular"/>
+            <param name="inputs" value="SRS014464-Anterior_nares-abundances.tabular,SRS014464-Anterior_nares-abundances-samefiledifferentname.tabular"/>
             <output name="output" ftype="tabular">
                 <assert_contents>
                     <has_text text="k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens"/>
-                    <has_text text="dataset_"/>
+                    <has_text text="SRS014464-Anterior_nares-abundances"/>
+                    <has_text text="SRS014464-Anterior_nares-abundances-samefiledifferentname"/>
                     <has_text text="clade_name"/>
                     <has_line_matching expression="#.*"/>
                 </assert_contents>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/SRS014464-Anterior_nares-abundances-samefiledifferentname.tabular	Sat Feb 10 23:56:53 2024 +0000
@@ -0,0 +1,31 @@
+#custom_db
+#mpa_v21_CHOCOPhlAnxxx_2
+#/home/bebatut/miniconda3/envs/mulled-v1-b4915a464cf72db4053ec566c65e3f5f431691323f08f9b6b1c9ecfc4f8b9c88/bin/metaphlan in --input_type fasta --read_min_len 70 --bowtie2db ref_db/ --index custom_db --bt2_ps very-sensitive --min_mapq_val 5 -t rel_ab --tax_lev a --min_cu_len 2000 --add_viruses --stat_q 0.2 --perc_nonzero 0.33 --avoid_disqm --sample_id_key SampleID --sample_id Metaphlan_Analysis -o /tmp/tmptu3575j7/files/000/dataset_19.dat --bowtie2out bowtie2out -s /tmp/tmptu3575j7/files/000/dataset_21.dat --biom /tmp/tmptu3575j7/files/000/dataset_22.dat --nproc 1
+#SampleID	Metaphlan_Analysis
+#clade_name	NCBI_tax_id	relative_abundance	additional_species
+k__Bacteria	2	100.0	
+k__Bacteria|p__Proteobacteria	2|1224	52.20019	
+k__Bacteria|p__Actinobacteria	2|201174	34.37371	
+k__Bacteria|p__Firmicutes	2|1239	13.4261	
+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria	2|1224|1236	52.20019	
+k__Bacteria|p__Actinobacteria|c__Actinobacteria	2|201174|1760	34.37371	
+k__Bacteria|p__Firmicutes|c__Bacilli	2|1239|91061	13.4261	
+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales	2|1224|1236|72274	52.20019	
+k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales	2|201174|1760|85007	24.7409	
+k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales	2|1239|91061|186826	13.4261	
+k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales	2|201174|1760|85009	9.63281	
+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae	2|1224|1236|72274|468	52.20019	
+k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae	2|201174|1760|85007|1653	24.7409	
+k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae	2|1239|91061|186826|186828	13.4261	
+k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae	2|201174|1760|85009|31957	9.63281	
+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella	2|1224|1236|72274|468|475	52.20019	
+k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium	2|201174|1760|85007|1653|1716	24.7409	
+k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum	2|1239|91061|186826|186828|29393	13.4261	
+k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium	2|201174|1760|85009|31957|1912216	9.63281	
+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_lacunata	2|1224|1236|72274|468|475|477	22.57968	
+k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_pseudodiphtheriticum	2|201174|1760|85007|1653|1716|37637	18.75365	
+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_nonliquefaciens	2|1224|1236|72274|468|475|478	15.88652	
+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_equi	2|1224|1236|72274|468|475|60442	13.73399	
+k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum|s__Dolosigranulum_pigrum	2|1239|91061|186826|186828|29393|29394	13.4261	
+k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium_acnes	2|201174|1760|85009|31957|1912216|1747	9.63281	
+k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens	2|201174|1760|85007|1653|1716|38284	5.98726