changeset 2:53dd00a4ab68 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 5078c7010ec46fd01fec2057dd4486781c958c37

--- a/blobtoolkit.xml	Mon Mar 20 16:37:54 2023 +0000
+++ b/blobtoolkit.xml	Tue Mar 28 15:17:19 2023 +0000
@@ -22,14 +22,16 @@
             --taxid $mode_conditional.taxid
             --taxdump './taxdump'
             './Blobdir'
-            && cp -r './taxdump' './Blobdir/'
-            && tar -zcf './Blobdir.tgz' './Blobdir'
-
+            && tar -C ./Blobdir -zcvf Blobdir.tgz .
         #else if $mode_conditional.selector == 'add'
+            mkdir -p './Blobdir' &&
+            mkdir -p './taxdump' &&
+            ln -s '${mode_conditional.taxdump}' 'taxdump.tar' &&
+            tar -xf 'taxdump.tar' -C './taxdump' &&
             #if $mode_conditional.blobdir.is_of_type("tgz")
-                tar -zxf '${mode_conditional.blobdir}' -C './' &&
+                tar -zxf '${mode_conditional.blobdir}' -C './Blobdir' &&
             #else
-                tar -xf '${mode_conditional.blobdir}' -C './' &&
+                tar -xf '${mode_conditional.blobdir}' -C './Blobdir' &&
             #end if
             #if $mode_conditional.busco
                 ln -s '${mode_conditional.busco}' './busco_results.tab' && 
@@ -50,7 +52,7 @@
             #end if
             blobtools add
                 --threads \${GALAXY_SLOTS:-8}
-                --taxdump './Blobdir/taxdump'
+                --taxdump './taxdump'
                 #if $mode_conditional.busco
                     --busco './busco_results.tab'
                 #end if
@@ -95,9 +97,15 @@
                 #end if
                 $mode_conditional.advanced_options.replace
                 './Blobdir'
-            && tar -zcf './Blobdir.tgz' './Blobdir'
+            && tar -C ./Blobdir -zcvf Blobdir.tgz .
 
         #else if $mode_conditional.selector == 'filter'
+            mkdir -p './Blobdir' &&
+            #if $mode_conditional.blobdir.is_of_type("tgz")
+                tar -zxf '${mode_conditional.blobdir}' -C './Blobdir' &&
+            #else
+                tar -xf '${mode_conditional.blobdir}' -C './Blobdir' &&
+            #end if
             #if $mode_conditional.filter_options.list
                     echo $mode_conditional.filter_options.list > id_list.txt &&
             #end if
@@ -148,29 +156,7 @@
                 #end if
                 ./Blobdir
             #end if
-            && tar -zcf './Blobdir.tgz' './Blobdir'
-
-        #else if $mode_conditional.selector == 'plots'
-            #if $mode_conditional.blobdir.is_of_type("tgz")
-                tar -zxf '${mode_conditional.blobdir}' -C './' &&
-            #else
-                tar -xf '${mode_conditional.blobdir}' -C './' &&
-            #end if            
-            blobtools view
-            --format $mode_conditional.format
-            --view 'blob'
-            ./Blobdir
-            && mv ./Blobdir.blob.circle* ./Blobdir.blob.circle
-            && blobtools view
-            --format $mode_conditional.format
-            --view 'cumulative'
-            ./Blobdir
-            && mv ./Blobdir.cumulative* Blobdir.cumulative
-            && blobtools view
-            --format $mode_conditional.format
-            --view 'snail'
-            ./Blobdir
-            && mv ./Blobdir.snail* Blobdir.snail
+            && tar -C ./Blobdir -zcvf Blobdir.tgz .
         #end if
     ]]></command>
     <inputs>
@@ -179,16 +165,16 @@
                 <option value="create">Create a BlobToolKit dataset</option>
                 <option value="add">Add data to a BlobToolKit dataset</option>
                 <option value="filter">Edit a BlobToolKit dataset</option>
-                <option value="plots">Generate plots</option>
             </param>
             <when value="create">
                 <param argument="--fasta" type="data" format="fasta" label="Genome assembly file" help="FASTA sequence file" />
                 <param argument="--meta" type="data" format="yaml" label="Metadata file" optional="true" help="Optional metadata dataset"/>
                 <param argument="--taxid" type="integer" value="" label="NCBI taxonomy ID" help="Add ranks to metadata for a taxid"/>
-                <param argument="--taxdump" type="data" format="tar,tgz,gz" label="NCBI taxdump directory" help="It should be compressed in tar.gz format"/>
+                <expand macro="macro_taxdump"/>
             </when>
             <when value="add">
                 <param name="blobdir" type="data" format="tgz" label="Blobdir.tgz file" help="This file should be generated by Blobtool create" />
+                <expand macro="macro_taxdump"/>
                 <param argument="--busco" type="data" format="tsv,tabular,txt" optional="true" label="BUSCO full table file"/>
                 <conditional name="blast_input">
                     <param name="selector" type="select" label="BLAST/Diamond hits">
@@ -310,38 +296,12 @@
                     </param>
                 </section>
             </when>
-            <when value="plots">
-                <param name="blobdir" type="data" format="tgz" label="Blobdir file" help="This file should be generated by the moudule create" />
-                <param argument="--format" type="select" label="Image format">
-                    <option value="png">PNG</option>
-                    <option value="svg">SVG</option>
-                </param>
-                <param argument="--param" type="text" optional="true" label="Query parameter" help="Query string parameter."/>
-            </when>
         </conditional>
     </inputs>
     <outputs>
         <data name="blobdir" format="tgz" from_work_dir="./Blobdir.tgz" label="${tool.name} on ${on_string}: Blobdir.tgz">
             <filter>mode_conditional['selector'] == 'create' or mode_conditional['selector'] == 'add' or mode_conditional['selector'] == 'filter'</filter>
         </data>
-        <data name="plot_circle" format="png" from_work_dir="./Blobdir.blob.circle" label="${tool.name} on ${on_string}: blob plot">
-            <filter>mode_conditional['selector'] == 'plots'</filter>
-            <change_format>
-                <when input="$mode_conditional.format" value="svg" format="svg"/>
-            </change_format>
-        </data>
-        <data name="plot_cumulative" format="png" from_work_dir="./Blobdir.cumulative" label="${tool.name} on ${on_string}: cumulative plot">
-            <filter>mode_conditional['selector'] == 'plots'</filter>
-            <change_format>
-                <when input="$mode_conditional.format" value="svg" format="svg"/>
-            </change_format>
-        </data>
-        <data name="plot_snail" format="png" from_work_dir="./Blobdir.snail" label="${tool.name} on ${on_string}: snail plot">
-            <filter>mode_conditional['selector'] == 'plots'</filter>
-            <change_format>
-                <when input="$mode_conditional.format" value="svg" format="svg"/>
-            </change_format>
-        </data>
     </outputs>
     <tests>
         <test expect_num_outputs="1">
@@ -352,12 +312,13 @@
                 <param name="taxid" value="801"/>
                 <param name="taxdump" value="small_taxdump.tar.gz"/>
             </conditional>
-            <output name="blobdir" file="test01_blobdir.tar.gz" compare="sim_size" delta="1500"/>
+            <output name="blobdir" file="test01_blobdir.tar.gz" compare="sim_size" delta="100"/>
         </test>
         <test expect_num_outputs="1">
             <conditional name="mode_conditional">
                 <param name="selector" value="add"/>
                 <param name="blobdir" value="test01_blobdir.tar.gz"/>
+                <param name="taxdump" value="small_taxdump.tar.gz"/>
                 <param name="busco" value="busco_full_table.tabular"/>
                 <param name="cov" value="bam_file.bam"/>
                 <param name="fasta" value="contig.fasta"/>
@@ -374,7 +335,7 @@
                     <param name="hits_cols" value="1=qseqid,2=staxids,3=bitscore,5=sseqid,10=qstart,11=qend,14=evalue"/>
                 </conditional>
             </conditional>
-            <output name="blobdir" file="test02_blobdir.tar.gz"  compare="sim_size" delta="1500"/>
+            <output name="blobdir" file="test02_blobdir.tar.gz"  compare="sim_size" delta="100"/>
         </test>
         <test expect_num_outputs="1">
             <conditional name="mode_conditional">
@@ -391,20 +352,10 @@
             </conditional>
             <output name="blobdir">
                 <assert_contents>
-                    <has_size value="672500" delta="1000"/>
+                    <has_size value="620" delta="50"/>
                 </assert_contents>
             </output>
         </test>
-        <test expect_num_outputs="3">
-            <conditional name="mode_conditional">
-                <param name="selector" value="plots"/>
-                <param name="blobdir" value="test02_blobdir.tar.gz"/>
-                <param name="format" value="png"/>
-            </conditional>
-            <output name="plot_circle" file="test04_circle.png" ftype="png"/>
-            <output name="plot_cumulative" file="test04_cumulative.png" ftype="png"/>
-            <output name="plot_snail" file="test04_snail.png" ftype="png"/>
-        </test>
         <test expect_num_outputs="1">
             <conditional name="mode_conditional">
                 <param name="selector" value="filter"/>
@@ -419,7 +370,7 @@
             </conditional>
             <output name="blobdir">
                 <assert_contents>
-                    <has_size value="672497" delta="1000"/>
+                    <has_size value="620" delta="50"/>
                 </assert_contents>
             </output>
         </test>
@@ -427,6 +378,13 @@
     <help><![CDATA[
     BlobToolKit is a software suite to aid researchers in identifying and isolating non-target data in draft and publicly available genome assemblies. It can be used to process assembly, 
     read and analysis files for fully reproducible interactive exploration in the browser-based Viewer. BlobToolKit can be used during assembly to filter non-target DNA, helping researchers produce assemblies with high biological credibility.
+
+.. class:: infomark
+    
+**NCBI taxdump directory**
+
+The taxdump database, provided by NCBI, includes the taxonomic lineage of taxa, information on type strains and material, and host information. The file **new_taxdump.tar.gz** can be downloaded from the taxonomy directory on the `FTP site <ftp.ncbi.nlm.nih.gov/pub/taxonomy/new_taxdump/>`_. 
+    
     ]]></help>
     <expand macro="citations"/>
-</tool>
\ No newline at end of file
+</tool>

--- a/macros.xml	Mon Mar 20 16:37:54 2023 +0000
+++ b/macros.xml	Tue Mar 28 15:17:19 2023 +0000
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">4.0.7</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     
     <xml name="requirements">
         <requirements>
@@ -42,6 +42,8 @@
             </when>
             <when value="disabled"/>
         </conditional>
-
+    </xml>
+    <xml name="macro_taxdump">
+        <param argument="--taxdump" type="data" format="tar,gz,tgz" label="NCBI taxdump directory" help="It requires to use the last taxdump version. You can find more information about it in the help section."/>
     </xml>
 </macros>

Binary file test-data/test01_blobdir.tar.gz has changed

Binary file test-data/test02_blobdir.tar.gz has changed