Mercurial > repos > florianbegusch > qiime2_suite

changeset 18:e1482b6ee5ed draft

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Uploaded
author florianbegusch
date Thu, 03 Sep 2020 11:02:29 +0000
parents 424d74a76037
children 6c48f8d82424
files qiime2/qiime_alignment_mafft.xml tool_data/qiime_rep_set.loc tool_data/qiime_taxonomy.loc tool_data_table_conf.xml.sample
diffstat 4 files changed, 74 insertions(+), 29 deletions(-) [+]
line wrap: on
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2/qiime_alignment_mafft.xml	Thu Sep 03 11:02:29 2020 +0000
@@ -0,0 +1,74 @@
+<?xml version="1.0" ?>
+<tool id="qiime_alignment_mafft" name="qiime alignment mafft"
+      version="2020.8">
+  <description>De novo multiple sequence alignment with MAFFT</description>
+  <requirements>
+    <requirement type="package" version="2020.8">qiime2</requirement>
+  </requirements>
+  <command><![CDATA[
+qiime alignment mafft
+
+--i-sequences=$isequences
+
+#if str($pnthreads) != 'None':
+--p-n-threads=$pnthreads
+#end if
+
+#if $pparttree:
+ --p-parttree
+#end if
+
+--o-alignment=oalignment
+
+#if str($examples) != 'None':
+--examples=$examples
+#end if
+
+;
+cp oalignment.qza $oalignment
+
+  ]]></command>
+  <inputs>
+    <param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT FeatureData[Sequence] The sequences to be aligned.              [required]" name="isequences" optional="False" type="data" />
+    <param label="--p-n-threads: " name="pnthreads" optional="True" type="select">
+      <option selected="True" value="None">Selection is Optional</option>
+      <option value="Int % Range(1">Int % Range(1</option>
+      <option value="None">None</option>
+    </param>
+    <param label="--p-parttree: --p-parttree: / --p-no-parttree This flag is required if the number of sequences being aligned are larger than 1000000. Disabled by default                             [default: False]" name="pparttree" selected="False" type="boolean" />
+    <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
+    
+  </inputs>
+
+  <outputs>
+    <data format="qza" label="${tool.name} on ${on_string}: alignment.qza" name="oalignment" />
+    
+  </outputs>
+
+  <help><![CDATA[
+De novo multiple sequence alignment with MAFFT
+###############################################################
+
+Perform de novo multiple sequence alignment using MAFFT.
+
+Parameters
+----------
+sequences : FeatureData[Sequence]
+    The sequences to be aligned.
+n_threads : Int % Range(1, None) | Str % Choices('auto'), optional
+    The number of threads. (Use `auto` to automatically use all available
+    cores)
+parttree : Bool, optional
+    This flag is required if the number of sequences being aligned are
+    larger than 1000000. Disabled by default
+
+Returns
+-------
+alignment : FeatureData[AlignedSequence]
+    The aligned sequences.
+  ]]></help>
+  <macros>
+    <import>qiime_citation.xml</import>
+  </macros>
+  <expand macro="qiime_citation"/>
+</tool>
\ No newline at end of file
--- a/tool_data/qiime_rep_set.loc	Thu Sep 03 10:53:49 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,9 +0,0 @@
-silva_132_release_rep_set_all_99_silva132_99	silva (132_release) - rep_set_all - 99 - 99_otus	silva_132_release_rep_set_all_99_silva132_99.fna	/home/galaxy/galaxy/tool-data/qiime_rep_set/silva_132_release_rep_set_all_99_silva132_99.fna
-silva_132_release_rep_set_all_97_silva132_97	silva (132_release) - rep_set_all - 97 - 97_otus	silva_132_release_rep_set_all_97_silva132_97.fna	/home/galaxy/galaxy/tool-data/qiime_rep_set/silva_132_release_rep_set_all_97_silva132_97.fna
-silva_128_release_rep_set_all_97_97_otus	silva (128_release) - rep_set_all - 97 - 97_otus	silva_128_release_rep_set_all_97_97_otus.fasta	/home/galaxy/galaxy/tool-data/qiime_rep_set/silva_128_release_rep_set_all_97_97_otus.fasta
-unite_20.11.2016_sh_refs_qiime_ver7_97_20.11.2016	unite (20.11.2016) - sh_refs_qiime_ver7_97_20	unite_20.11.2016_sh_refs_qiime_ver7_97_20.11.2016.fasta	/home/galaxy/galaxy/tool-data/qiime_rep_set/unite_20.11.2016_sh_refs_qiime_ver7_97_20.11.2016.fasta
-greengenes_13_8_97_otus	greengenes (13_8_relese) - 97_otus	greengenes_13_8_97_otus.fasta	/home/galaxy/galaxy/tool-data/qiime_rep_set/greengenes_13_8_97_otus.fasta
-greengenes_13_8_99_otus	greengenes (13_8_relese) - 99_otus	greengenes_13_8_99_otus.fasta	/home/galaxy/galaxy/tool-data/qiime_rep_set/greengenes_13_8_99_otus.fasta
-GreenGenes_13_8_99_V4_GTGCCAGCMGCCGCGGTAA_GGACTACHVHHHTWTCTAAT	GreenGenes_13_8_99_V4_GTGCCAGCMGCCGCGGTAA_GGACTACHVHHHTWTCTAAT	GreenGenes_13_8_99_V4_GTGCCAGCMGCCGCGGTAA_GGACTACHVHHHTWTCTAAT.qza	/home/galaxy/galaxy/tool-data/QIIME2_reference_classifiers/GreenGenes_13_8_99_V4_GTGCCAGCMGCCGCGGTAA_GGACTACHVHHHTWTCTAAT.qza
-GreenGenes_13_8_99_V4_GTGYCAGCMGCCGCGGTAA_GGACTACNVGGGTWTCTAAT	GreenGenes_13_8_99_V4_GTGYCAGCMGCCGCGGTAA_GGACTACNVGGGTWTCTAAT	GreenGenes_13_8_99_V4_GTGYCAGCMGCCGCGGTAA_GGACTACNVGGGTWTCTAAT.qza	/home/galaxy/galaxy/tool-data/QIIME2_reference_classifiers/GreenGenes_13_8_99_V4_GTGYCAGCMGCCGCGGTAA_GGACTACNVGGGTWTCTAAT.qza
-GreenGenes_13_8_97_V1_V2_AGAGTTTGATCCTGGCTCAG_CTGCTGCCTYCCGTA	GreenGenes_13_8_97_V1_V2_AGAGTTTGATCCTGGCTCAG_CTGCTGCCTYCCGTA	GreenGenes_13_8_97_V1_V2_AGAGTTTGATCCTGGCTCAG_CTGCTGCCTYCCGTA.qza	/home/galaxy/galaxy/tool-data/QIIME2_reference_classifiers/GreenGenes_13_8_97_V1_V2_AGAGTTTGATCCTGGCTCAG_CTGCTGCCTYCCGTA.qza
--- a/tool_data/qiime_taxonomy.loc	Thu Sep 03 10:53:49 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,8 +0,0 @@
-silva_132_release_taxonomy_all_99_taxonomy_all_levels	silva (132_release) - taxonomy_all - 99 - taxonomy_all_levels	silva_132_release_taxonomy_all_99_taxonomy_all_levels.txt	/home/galaxy/galaxy/tool-data/qiime_taxonomy/silva_132_release_taxonomy_all_99_taxonomy_all_levels.txt	
-silva_132_release_taxonomy_all_97_taxonomy_all_levels	silva (132_release) - taxonomy_all - 97 - taxonomy_all_levels	silva_132_release_taxonomy_all_97_taxonomy_all_levels.txt	/home/galaxy/galaxy/tool-data/qiime_taxonomy/silva_132_release_taxonomy_all_97_taxonomy_all_levels.txt	
-greengenes_13_8_97_otu_taxonomy	greengenes (13_8) - 97_otu_taxonomy	greengenes_13_8_97_otu_taxonomy.txt	/home/galaxy/galaxy/tool-data/qiime_taxonomy/greengenes_13_8_97_otu_taxonomy.txt	
-greengenes_13_8_99_otu_taxonomy	greengenes (13_8) - 99_otu_taxonomy	greengenes_13_8_99_otu_taxonomy.txt	/home/galaxy/galaxy/tool-data/qiime_taxonomy/greengenes_13_8_99_otu_taxonomy.txt	
-silva_128_release_taxonomy_all_97_taxonomy_all_levels	silva (128_release) - taxonomy_all - 97 - taxonomy_all_levels	silva_128_release_taxonomy_all_97_taxonomy_all_levels.txt	/home/galaxy/galaxy/tool-data/qiime_taxonomy/silva_128_release_taxonomy_all_97_taxonomy_all_levels.txt	
-unite_20.11.2016_sh_taxonomy_qiime_ver7_97_20.11.2016	unite (20.11.2016) - sh_taxonomy_qiime_ver7_97_20	unite_20.11.2016_sh_taxonomy_qiime_ver7_97_20.11.2016.txt	/home/galaxy/galaxy/tool-data/qiime_taxonomy/unite_20.11.2016_sh_taxonomy_qiime_ver7_97_20.11.2016.txt	
-taxmap_ncbi_ssu_ref_132	taxmap_ncbi_ssu_ref_132	taxmap_ncbi_ssu_ref_132.txt	/home/galaxy/galaxy/tool-data/qiime_taxonomy/taxmap_ncbi_ssu_ref_132.txt	
-taxmap_slv_ssu_ref_132	taxmap_slv_ssu_ref_132	taxmap_slv_ssu_ref_132.txt	/home/galaxy/galaxy/tool-data/qiime_taxonomy/taxmap_slv_ssu_ref_132.txt	
--- a/tool_data_table_conf.xml.sample	Thu Sep 03 10:53:49 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,12 +0,0 @@
-<tables>
-    <table name="taxonomy_fp" comment_char="#">
-        <columns>value, name, dbkey, path</columns>
-        <file path="tool_data/qiime_rep_set.loc" />
-    </table>
-    <table name="classifier_fp" comment_char="#">
-        <columns>value, name, dbkey, path</columns>
-        <file path="tool-data/qiime_taxonomy.loc" />
-    </table>
-</tables>
-
-