Mercurial > repos > iuc > data_manager_mothur_toolsuite

diff data_manager/data_manager_fetch_mothur_reference_data.xml @ 2:0e532fc0a0a6 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_mothur_toolsuite/ commit b824ec6d0faa5353c5893b5a2a540b8251cae309"
author iuc
date Thu, 17 Sep 2020 09:37:41 +0000
parents aec831b54a5b
children 0db22932bc39
line wrap: on
line diff
--- a/data_manager/data_manager_fetch_mothur_reference_data.xml	Thu Nov 28 15:47:32 2019 -0500
+++ b/data_manager/data_manager_fetch_mothur_reference_data.xml	Thu Sep 17 09:37:41 2020 +0000
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="data_manager_fetch_mothur_reference_data" name="Fetch Mothur toolsuite reference data" version="0.1.4" tool_type="manage_data" profile="19.05">
+<tool id="data_manager_fetch_mothur_reference_data" name="Fetch Mothur toolsuite reference data" version="0.1.5" tool_type="manage_data" profile="19.05">
     <description>Fetch and install reference data for Mothur</description>
     <requirements>
         <requirement type="package" version="2.7">python</requirement>
@@ -74,6 +74,223 @@
                 </assert_contents>
             </output>
         </test>
+        <test>
+            <param name="data_source|ref_data" value="lookup_gsflx"/>
+            <output name="out_file">
+                <assert_contents>
+                    <has_text text="GSFLX" />
+                    <has_text text="LookUp_GSFLX.pat" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="data_source|ref_data" value="lookup_gs20"/>
+            <output name="out_file">
+                <assert_contents>
+                    <has_text text="GS20" />
+                    <has_text text="LookUp_GS20.pat" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="data_source|ref_data" value="RDP_v16"/>
+            <output name="out_file">
+                <assert_contents>
+                    <has_text text="16S rRNA RDP training set 16" />
+                    <has_text text="trainset16_022016.rdp.fasta" />
+                    <has_text text="trainset16_022016.rdp.tax" />
+                    <has_text text="trainset16_022016.pds.fasta" />
+                    <has_text text="trainset16_022016.pds.tax" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="data_source|ref_data" value="RDP_v14"/>
+            <output name="out_file">
+                <assert_contents>
+                    <has_text text="16S rRNA RDP training set 14" />
+                    <has_text text="trainset14_032015.rdp.fasta" />
+                    <has_text text="trainset14_032015.rdp.tax" />
+                    <has_text text="trainset14_032015.pds.fasta" />
+                    <has_text text="trainset14_032015.pds.tax" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="data_source|ref_data" value="RDP_v10"/>
+            <output name="out_file">
+                <assert_contents>
+                    <has_text text="16S rRNA RDP training set 10" />
+                    <has_text text="trainset10_082014.rdp.fasta" />
+                    <has_text text="trainset10_082014.rdp.tax" />
+                    <has_text text="trainset10_082014.pds.fasta" />
+                    <has_text text="trainset10_082014.pds.tax" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="data_source|ref_data" value="RDP_v9"/>
+            <output name="out_file">
+                <assert_contents>
+                    <has_text text="16S rRNA PDS training set 9" />
+                    <has_text text="trainset9_032012.rdp.fasta" />
+                    <has_text text="trainset9_032012.rdp.tax" />
+                    <has_text text="trainset9_032012.pds.fasta" />
+                    <has_text text="trainset9_032012.pds.tax" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="data_source|ref_data" value="RDP_v7"/>
+            <output name="out_file">
+                <assert_contents>
+                    <has_text text="16S rRNA RDP training set 7" />
+                    <has_text text="FungiLSU_train_1400bp_8506_mod.fasta" />
+                    <has_text text="FungiLSU_train_1400bp_8506_mod.tax" />
+                    <has_text text="trainset7_112011.rdp.fasta" />
+                    <has_text text="trainset7_112011.rdp.tax" />
+                    <has_text text="trainset7_112011.pds.fasta" />
+                    <has_text text="trainset7_112011.pds.tax" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="data_source|ref_data" value="RDP_v6"/>
+            <output name="out_file">
+                <assert_contents>
+                    <has_text text="RDP training set 6" />
+                    <has_text text="trainset6_032010.rdp.fasta" />
+                    <has_text text="trainset6_032010.rdp.tax" />
+                </assert_contents>
+            </output>
+        </test>
+        <!-- SILVA data is to large (>1GB each) for CI testing on github actions
+             so we skip them -->
+        <!--<test>
+            <param name="data_source|ref_data" value="silva_release_128"/>
+            <output name="out_file">
+                <assert_contents>
+                    <has_text text="SILVA release 128" />
+                    <has_text text="silva.nr_v128.tax" />
+                    <has_text text="silva.seed_v128.tax" />
+                    <has_text text="silva.nr_v128.align" />
+                    <has_text text="silva.seed_v128.align" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="data_source|ref_data" value="silva_release_123"/>
+            <output name="out_file">
+                <assert_contents>
+                    <has_text text="SILVA release 123" />
+                    <has_text text="silva.nr_v123.align" />
+                    <has_text text="silva.seed_v123.align" />
+                    <has_text text="silva.nr_v123.tax" />
+                    <has_text text="silva.seed_v123.tax" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="data_source|ref_data" value="silva_release_119"/>
+            <output name="out_file">
+                <assert_contents>
+                    <has_text text="SILVA release 119" />
+                    <has_text text="silva.nr_v119.align" />
+                    <has_text text="silva.seed_v119.align" />
+                    <has_text text="silva.nr_v119.tax" />
+                    <has_text text="silva.seed_v119.tax" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="data_source|ref_data" value="silva_release_102"/>
+            <output name="out_file">
+                <assert_contents>
+                    <has_text text="SILVA release 102" />
+                    <has_text text="silva.bacteria.fasta" />
+                    <has_text text="silva.gold.ng.fasta" />
+                    <has_text text="nogap.archaea.fasta" />
+                    <has_text text="silva.archaea.fasta" />
+                    <has_text text="nogap.eukarya.fasta" />
+                    <has_text text="silva.eukarya.fasta" />
+                    <has_text text="silva.bacteria.gg.tax" />
+                    <has_text text="silva.bacteria.ncbi.tax" />
+                    <has_text text="silva.bacteria.rdp.tax" />
+                    <has_text text="silva.bacteria.rdp6.tax" />
+                    <has_text text="silva.bacteria.silva.tax" />
+                    <has_text text="silva.archaea.gg.tax" />
+                    <has_text text="silva.archaea.ncbi.tax" />
+                    <has_text text="silva.archaea.rdp.tax" />
+                    <has_text text="silva.archaea.silva.tax" />
+                    <has_text text="silva.eukarya.ncbi.tax" />
+                    <has_text text="silva.eukarya.silva.tax" />
+                </assert_contents>
+            </output>
+        </test>-->
+
+        <!-- also greengenes is large (400MB-1.5GB) so only tests for older
+             (smaller) releases are executed -->
+        <!--<test>
+            <param name="data_source|ref_data" value="greengenes_August2013"/>
+            <output name="out_file">
+                <assert_contents>
+                    <has_text text="Greengenes August 2013" />
+                    <has_text text="gg_13_8_99.gg.tax" />
+                    <has_text text="gg_13_8_99.fasta" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="data_source|ref_data" value="greengenes_May2013"/>
+            <output name="out_file">
+                <assert_contents>
+                    <has_text text="Greengenes May 2013" />
+                    <has_text text="gg_13_5_99.pds.tax" />
+                    <has_text text="gg_13_5_99.gg.tax" />
+                    <has_text text="gg_13_5_99.align" />
+                    <has_text text="gg_13_5_99.fasta" />
+                </assert_contents>
+            </output>
+        </test>-->
+        <test>
+            <param name="data_source|ref_data" value="greengenes_old"/>
+            <output name="out_file">
+                <assert_contents>
+                    <has_text text="Greengenes pre-May 2013" />
+                    <has_text text="gg_99.pds.tax" />
+                    <has_text text="core_set_aligned.imputed.fasta" />
+                    <has_text text="gg_99.pds.ng.fasta" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="data_source|ref_data" value="greengenes_gold_alignment"/>
+            <output name="out_file">
+                <assert_contents>
+                    <has_text text="Greengenes gold alignment" />
+                    <has_text text="rRNA16S.gold.NAST_ALIGNED.fasta" />
+                </assert_contents>
+            </output>
+        </test>
+
+        <test>
+            <param name="data_source|ref_data" value="secondary_structure_maps_silva"/>
+            <output name="out_file">
+                <assert_contents>
+                    <has_text text="SILVA" />
+                    <has_text text="silva.ss.map" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="data_source|ref_data" value="secondary_structure_maps_greengenes"/>
+            <output name="out_file">
+                <assert_contents>
+                    <has_text text="Greengenes" />
+                    <has_text text="gg.ss.map" />
+                </assert_contents>
+            </output>
+        </test>
     </tests>
     <help>
 .. class:: infomark