diff blobtoolkit.xml @ 1:840822c1e84a draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 797eb67eae4dfe502325c53f78824c5ba4033955

--- a/blobtoolkit.xml	Mon Jan 30 12:39:40 2023 +0000
+++ b/blobtoolkit.xml	Mon Mar 20 16:37:54 2023 +0000
@@ -39,7 +39,6 @@
             #end if
             #if $mode_conditional.cov
                 ln -s '$mode_conditional.cov' './input.bam' &&
-                ln -s '$mode_conditional.cov.metadata.bam_index' './input.bam.bai' &&
             #end if
             #if $mode_conditional.bed
                     mkdir -p './bed_files' &&
@@ -99,6 +98,9 @@
             && tar -zcf './Blobdir.tgz' './Blobdir'
 
         #else if $mode_conditional.selector == 'filter'
+            #if $mode_conditional.filter_options.list
+                    echo $mode_conditional.filter_options.list > id_list.txt &&
+            #end if
             #if $mode_conditional.blobdir.is_of_type("tgz")
                 tar -zxf '${mode_conditional.blobdir}' -C './' &&
             #else
@@ -108,9 +110,8 @@
                 ln -s '${mode_conditional.filter_options.fasta}' './input.fasta' &&
             #end if
             #if $mode_conditional.filter_options.fastq_filter.selector == 'enabled'
-                ln -s '${mode_conditional.filter_options.fastq}' './input.fastq' &&
-                ln -s '$mode_conditional.filter_options.cov' './input.bam' &&
-                ln -s '$mode_conditional.filter_options.cov.metadata.bam_index' './input.bam.csi' &&
+                ln -s '${mode_conditional.filter_options.fastq_filter.fastq}' './input.fastq' &&
+                ln -s '$mode_conditional.filter_options.fastq_filter.cov' './input.bam' &&
             #end if
             blobtools filter
             #if $mode_conditional.filter_options.param
@@ -120,7 +121,7 @@
                 --json $mode_conditional.filter_options.json
             #end if
             #if $mode_conditional.filter_options.list
-                --list $mode_conditional.filter_options.list
+                --list id_list.txt
             #end if
             $mode_conditional.filter_options.invert
             #if $mode_conditional.filter_options.fasta
@@ -351,7 +352,7 @@
                 <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="1000"/>
+            <output name="blobdir" file="test01_blobdir.tar.gz" compare="sim_size" delta="1500"/>
         </test>
         <test expect_num_outputs="1">
             <conditional name="mode_conditional">
@@ -373,7 +374,7 @@
                     <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="1000"/>
+            <output name="blobdir" file="test02_blobdir.tar.gz"  compare="sim_size" delta="1500"/>
         </test>
         <test expect_num_outputs="1">
             <conditional name="mode_conditional">
@@ -390,7 +391,7 @@
             </conditional>
             <output name="blobdir">
                 <assert_contents>
-                    <has_size value="672428" delta="1000"/>
+                    <has_size value="672500" delta="1000"/>
                 </assert_contents>
             </output>
         </test>
@@ -404,6 +405,24 @@
             <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"/>
+                <param name="blobdir" value="test02_blobdir.tar.gz"/>
+                <section name="filter_options">
+                    <param name="list" value="801 802"/>
+                    <param name="fasta" value="contig.fasta"/>
+                </section>
+                <section name="remove_options">
+                    <param name="remove_selector" value="--all"/>
+                </section>
+            </conditional>
+            <output name="blobdir">
+                <assert_contents>
+                    <has_size value="672497" delta="1000"/>
+                </assert_contents>
+            </output>
+        </test>
     </tests>
     <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,