# HG changeset patch
# User jjohnson
# Date 1585620379 14400
# Node ID eddf2f556a9222ef5bee337a349f7031836675c7
# Parent  42d0c1c21cd47e10fe7eb97e7b1372d669e0f759
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/transindel commit af32e767fd29667d3e29f1a202ad59d3dd498c84-dirty"

diff -r 42d0c1c21cd4 -r eddf2f556a92 transindel.xml
--- a/transindel.xml	Fri Mar 27 12:06:25 2020 -0400
+++ b/transindel.xml	Mon Mar 30 22:06:19 2020 -0400
@@ -6,13 +6,15 @@
     <expand macro="requirements" />
     <expand macro="version_command" />
     <command detect_errors="exit_code"><![CDATA[
+        ln -s -f '${analyze.input}' 'input.bam' &&
+        ln -s -f '${analyze.input.metadata.bam_index}' 'input.bai' &&
         #if $analyze.input_src == 'RNA'
             #if $analyze.rfasta.rfasta_source == "history":
                 ln -s '$analyze.rfasta.ref_fa_hist' ref.fa &&
             #else:
                 ln -s '$analyze.rfasta.ref_fa_builtin.fields.path' ref.fa &&
             #end if
-            transIndel_build_RNA.py -i '$analyze.input' -o 'transIndel.bam'
+            transIndel_build_RNA.py -i 'input.bam' -o 'transIndel.bam'
             ## Get reference FASTA
             -r ref.fa
             ## Get reference GTF
@@ -36,7 +38,7 @@
                    #end if
             #end if
         #elif $analyze.input_src == 'DNA'
-            transIndel_build_DNA.py -i '$analyze.input' -o 'transIndel.bam'
+            transIndel_build_DNA.py -i 'input.bam' -o 'transIndel.bam'
             --mapq_cutoff $analyze.mapq_cutoff
             --max_del_length $analyze.max_del_length
             #if $analyze.transIndel_call.run_transIndel_call == 'yes'
@@ -62,8 +64,8 @@
             #else:
                 ln -s '$analyze.rfasta.ref_fa_builtin.fields.path' ref.fa &&
             #end if
-            transIndel_call.py -i '$analyze.input' -o 'transIndel'
-                   -r re.fasta
+            transIndel_call.py -i 'input.bam' -o 'transIndel'
+                   -r ref.fa
 		   -c $analyze.call_opts.min_observation_count
                    -d $analyze.call_opts.min_depth
                    -f $analyze.call_opts.min_allele_frequency
@@ -105,10 +107,10 @@
     </inputs>
     <outputs>
         <data name="output_bam" format="bam" label="${tool.name} on ${on_string}: transIndel.bam" from_work_dir="transIndel.bam">
-            <filter>analyze['input_src'] != 'transindel' </filter>
+            <filter>analyze['input_src'] != 'transIndel'</filter>
         </data>
         <data name="output_vcf" format="vcf" label="${tool.name} on ${on_string}: transIndel.indel.vcf" from_work_dir="transIndel.indel.vcf" >
-            <filter>analyze['input_src'] == 'transindel' or analyze['transIndel_call']['run_transIndel_call'] == 'yes'</filter>
+            <filter>analyze['input_src'] == 'transIndel' or analyze['transIndel_call']['run_transIndel_call'] == 'yes'</filter>
         </data>
     </outputs>
     <tests>