# HG changeset patch
# User iuc
# Date 1631257140 0
# Node ID 6cc65a11d922eda5c31e9f34f1a3f74e2d2c05e0
# Parent  ec5a925141137dd2acba012a8046e692b5b1b034
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fsd commit db742c73b55c12a5ac5a11e6be3995670547bbb0"

diff -r ec5a92514113 -r 6cc65a11d922 fsd_beforevsafter.py
--- a/fsd_beforevsafter.py	Wed Dec 04 16:32:40 2019 -0500
+++ b/fsd_beforevsafter.py	Fri Sep 10 06:59:00 2021 +0000
@@ -13,6 +13,7 @@
 # --output_tabular outputfile_name_tabular --output_pdf outputfile_name_pdf
 
 import argparse
+import os.path
 import sys
 from collections import Counter
 
@@ -164,7 +165,10 @@
 
         # data of tags aligned to reference genome
         if ref_genome is not None:
-            pysam.index(ref_genome)
+            ref_genome_index = f"{ref_genome}.bai"
+            if not os.path.exists(ref_genome_index):
+                print(f"Info: Generating BAM index in {ref_genome_index}")
+                pysam.index(ref_genome)
             bam = pysam.AlignmentFile(ref_genome, "rb")
             seq_mut = []
             for read in bam.fetch():
diff -r ec5a92514113 -r 6cc65a11d922 fsd_beforevsafter.xml
--- a/fsd_beforevsafter.xml	Wed Dec 04 16:32:40 2019 -0500
+++ b/fsd_beforevsafter.xml	Fri Sep 10 06:59:00 2021 +0000
@@ -8,7 +8,11 @@
         <requirement type="package" version="1.71">biopython</requirement>
         <requirement type="package" version="0.15">pysam</requirement>
     </expand>
-    <command>
+    <command><![CDATA[
+#if $bamFile:
+    ln -s '$bamFile' 'reads.bam' &&
+    ln -s '$bamFile.metadata.bam_index' 'reads.bam.bai' &&
+#end if
 python '$__tool_directory__/fsd_beforevsafter.py'
 --inputFile_SSCS '$file'
 --inputName1 @ESCAPE_IDENTIFIER@
@@ -17,11 +21,11 @@
     --afterTrimming '$afterTrimming'
 #end if
 #if $bamFile:
---bamFile '$bamFile'
+    --bamFile 'reads.bam'
 #end if
 --output_pdf '$output_pdf'
 --output_tabular '$output_tabular'
-    </command>
+    ]]></command>
     <inputs>
         <param name="file" type="data" format="tabular" label="Input tags of SSCSs" optional="false" help="This dataset is generated by post-processing of the output from 'Make Families' or 'Correct Barcodes' tool by extracting the first two columns, sorting the tags (column 1) and adding the counts of unique occurencies of each tag. See Help section below for a detailed explanation."/>
         <param name="makeDCS" type="data" format="fasta" label="Input tags after making DCSs" help="Input in fasta format with the tags of the reads, which were aligned to DCSs. This file is produced by the 'Make consensus reads' tool."/>
diff -r ec5a92514113 -r 6cc65a11d922 fsd_regions.py
--- a/fsd_regions.py	Wed Dec 04 16:32:40 2019 -0500
+++ b/fsd_regions.py	Fri Sep 10 06:59:00 2021 +0000
@@ -17,6 +17,7 @@
 
 import argparse
 import collections
+import os.path
 import re
 import sys
 
@@ -61,7 +62,10 @@
 
     with open(title_file2, "w") as output_file, PdfPages(title_file) as pdf:
         data_array = readFileReferenceFree(firstFile, "\t")
-        pysam.index(bamFile)
+        bamIndex = f"{bamFile}.bai"
+        if not os.path.exists(bamIndex):
+            print(f"Info: Generating BAM index in {bamIndex}")
+            pysam.index(bamFile)
 
         bam = pysam.AlignmentFile(bamFile, "rb")
         qname_dict = collections.OrderedDict()
diff -r ec5a92514113 -r 6cc65a11d922 fsd_regions.xml
--- a/fsd_regions.xml	Wed Dec 04 16:32:40 2019 -0500
+++ b/fsd_regions.xml	Fri Sep 10 06:59:00 2021 +0000
@@ -7,17 +7,19 @@
     <expand macro="requirements" >
         <requirement type="package" version="0.15">pysam</requirement>
     </expand>
-    <command>
+    <command><![CDATA[
+ln -s '$file2' 'reads.bam' &&
+ln -s '$file2.metadata.bam_index' 'reads.bam.bai' &&
 python '$__tool_directory__/fsd_regions.py'
 --inputFile '$file'
 --inputName1 @ESCAPE_IDENTIFIER@
---bamFile '$file2'
+--bamFile 'reads.bam'
 #if $file3:
     --rangesFile '$file3'
 #end if
 --output_pdf '$output_pdf'
 --output_tabular '$output_tabular'
-    </command>
+    ]]></command>
     <inputs>
         <param name="file" type="data" format="tabular" label="Input tags of whole dataset" optional="false" help="This dataset is generated by post-processing of the output from 'Make Families' or 'Correct Barcodes' tool by extracting the first two columns, sorting the tags (column 1) and adding the counts of unique occurencies of each tag. See Help section below for a detailed explanation."/>
         <param name="file2" type="data" format="bam" label="BAM file of aligned reads." help="Input in BAM format with the reads that were aligned to the reference genome."/>