Mercurial > repos > iuc > chira_merge
diff chira_merge.xml @ 7:35f433d0bd7f draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit ac10509d952583cefd7bf63910cd6976a0124440"
| author | iuc |
|---|---|
| date | Thu, 07 May 2020 03:35:27 -0400 |
| parents | 0170de5072d4 |
| children | c836a05bd6a3 |
line wrap: on
line diff
--- a/chira_merge.xml Thu Apr 16 13:23:11 2020 -0400 +++ b/chira_merge.xml Thu May 07 03:35:27 2020 -0400 @@ -20,6 +20,11 @@ #else: -ao '$merge.alignment_overlap' #end if + #if str($reference.ref_type) == "split": + -f1 '$reference.ref_fasta1' + -f2 '$reference.ref_fasta2' + #end if + $chimeric_only -o ./ ]]></command> @@ -59,6 +64,22 @@ help="scale stddev for a single read"/> </when> </conditional> + <conditional name="reference"> + <param name="ref_type" type="select" label="Did you use single or split reference for alignment?"> + <option value="single">Single reference</option> + <option value="split">Split reference</option> + </param> + <when value="split"> + <param format="fasta" name="ref_fasta1" type="data" label="Reference FASTA file" + help="Reference fasta file"/> + <param format="fasta" name="ref_fasta2" type="data" label="Second reference FASTA file" + help="Second reference fasta file."/> + </when> + <when value="single"> + <!-- no need to provide a fasta file --> + </when> + </conditional> + <param name="chimeric_only" type="boolean" truevalue="-c" falsevalue="" checked="false" /> </inputs> <outputs> <data format="bed" name="segments_bed" from_work_dir="segments.bed" label="ChiRA aligned read segments on ${on_string}"/> @@ -70,15 +91,18 @@ <test expect_num_outputs="2"> <param name="alignments" value="alignments.bed"/> <param name="choice" value="no" /> + <param name="ref_type" value="split"/> + <param name="ref_fasta1" value="ref1.fasta"/> + <param name="ref_fasta2" value="ref2.fasta"/> <output name="segments_bed" > <assert_contents> - <has_text_matching expression="ENSMUST00000160533\t69\t82\t34\|1\|2,ENSMUST00000160533,69,82,\+,42S13M\t1\t\+" /> + <has_text_matching expression="ENSMUST00000146006\t6703\t6718\t10\|2\|3,ENSMUST00000146006,6703,6718,\+,24S15M16S\t1\t\+" /> </assert_contents> </output> <output name="merged_bed" > <assert_contents> <has_text_matching expression="ENSMUST00000182010\t408\t477\t\+" /> - <has_text_matching expression="mmu-miR-106a-3p\t4\t15\t\+" /> + <has_text_matching expression="mmu-miR-9-5p\t0\t23\t\+" /> </assert_contents> </output> </test> @@ -87,15 +111,19 @@ <param name="alignments" value="alignments.bed" /> <param name="choice" value="yes" /> <param name="gtf" value="annotation.gtf" /> + <param name="ref_type" value="split"/> + <param name="ref_fasta1" value="ref1.fasta"/> + <param name="ref_fasta2" value="ref2.fasta"/> <output name="segments_bed" > <assert_contents> - <has_text_matching expression="5\t137142331\t137142344\t34\|1\|2,ENSMUST00000160533,69,82,\+,42S13M\t1\t-" /> + <has_text_matching expression="2\t31033086\t31033109\t38\|2\|2,ENSMUST00000113555,1676,1699,\+,32S23M\t1\t-" /> + <has_text_matching expression="7\t83738820\t83738843\t38\|2\|1,mmu-miR-9-5p,0,23,\+,5S23M27S\t1\t\+" /> </assert_contents> </output> <output name="merged_bed" > <assert_contents> - <has_text_matching expression="17\t39846957\t39847016\t\+" /> - <has_text_matching expression="5\t137142331\t137142344\t-" /> + <has_text_matching expression="2\t31033086\t31033109\t-" /> + <has_text_matching expression="7\t83738820\t83738843\t\+" /> </assert_contents> </output> </test> @@ -106,14 +134,39 @@ <param name="gtf" value="annotation.gtf" /> <param name="mode" value="blockbuster" /> <param name="min_cluster_height" value="5" /> + <param name="ref_type" value="split"/> + <param name="ref_fasta1" value="ref1.fasta"/> + <param name="ref_fasta2" value="ref2.fasta"/> <output name="segments_bed" > <assert_contents> - <has_text_matching expression="5\t137142331\t137142344\t34\|1\|2,ENSMUST00000160533,69,82,\+,42S13M\t1\t-" /> + <has_text_matching expression="2\t31033086\t31033109\t38\|2\|2,ENSMUST00000113555,1676,1699,\+,32S23M\t1\t-" /> + <has_text_matching expression="7\t83738820\t83738843\t38\|2\|1,mmu-miR-9-5p,0,23,\+,5S23M27S\t1\t\+" /> </assert_contents> </output> <output name="merged_bed" > <assert_contents> - <has_text_matching expression="17\t39846957\t39847016\t\+" /> + <has_text_matching expression="7\t83738820\t83738843\t\+" /> + </assert_contents> + </output> + </test> + <!-- Test: Chimeric only without annotation --> + <test expect_num_outputs="2"> + <param name="alignments" value="alignments.bed"/> + <param name="choice" value="no" /> + <param name="ref_type" value="split"/> + <param name="ref_fasta1" value="ref1.fasta"/> + <param name="ref_fasta2" value="ref2.fasta"/> + <param name="chimeric_only" value="true"/> + <output name="segments_bed" > + <assert_contents> + <has_text_matching expression="mmu-miR-9-5p\t0\t23\t38\|2\|1,mmu-miR-9-5p,0,23,\+,5S23M27S\t1\t\+" /> + <has_text_matching expression="ENSMUST00000113555\t1676\t1699\t38\|2\|2,ENSMUST00000113555,1676,1699,\+,32S23M\t1\t\+" /> + </assert_contents> + </output> + <output name="merged_bed" > + <assert_contents> + <has_text_matching expression="ENSMUST00000113555\t1676\t1699\t\+" /> + <has_text_matching expression="mmu-miR-9-5p\t0\t23\t\+" /> </assert_contents> </output> </test>