avoid bam2msa to create BAM index in inputdir (#3986)
avoid bam2msa to create BAM index in inputdir (#3986)

* avoid bam2msa to create BAM index in inputdir

* add input_bam in tool run

* also link in index files

Co-authored-by: Björn Grüning <a31805f6001ab3b535ea95133fbc4db46e97e8d1@gruenings.eu>
loraine-gueguen/tools-iuc,mvdbeek/tools-iuc,pavanvidem/tools-iuc,galaxyproject/tools-iuc,gregvonkuster/tools-iuc,blankenberg/tools-iuc,ieguinoa/tools-iuc,galaxyproject/tools-iuc,abretaud/tools-iuc,loraine-gueguen/tools-iuc,nekrut/tools-iuc,mvdbeek/tools-iuc,galaxyproject/tools-iuc,natefoo/tools-iuc,davebx/tools-iuc,davebx/tools-iuc,loraine-gueguen/tools-iuc,ieguinoa/tools-iuc,pavanvidem/tools-iuc,nsoranzo/tools-iuc,abretaud/tools-iuc,pavanvidem/tools-iuc,davebx/tools-iuc,Delphine-L/tools-iuc,davebx/tools-iuc,abretaud/tools-iuc,gregvonkuster/tools-iuc,davebx/tools-iuc,ieguinoa/tools-iuc,natefoo/tools-iuc,pavanvidem/tools-iuc,davebx/tools-iuc,abretaud/tools-iuc,mvdbeek/tools-iuc,galaxyproject/tools-iuc,blankenberg/tools-iuc,pavanvidem/tools-iuc,gregvonkuster/tools-iuc,Delphine-L/tools-iuc,natefoo/tools-iuc,abretaud/tools-iuc,blankenberg/tools-iuc,natefoo/tools-iuc,blankenberg/tools-iuc,nsoranzo/tools-iuc,nsoranzo/tools-iuc,pavanvidem/tools-iuc,blankenberg/tools-iuc,Delphine-L/tools-iuc,jj-umn/tools-iuc,loraine-gueguen/tools-iuc,Delphine-L/tools-iuc,nekrut/tools-iuc,jj-umn/tools-iuc,blankenberg/tools-iuc,loraine-gueguen/tools-iuc,nsoranzo/tools-iuc,nekrut/tools-iuc,mvdbeek/tools-iuc,nekrut/tools-iuc,mvdbeek/tools-iuc,mvdbeek/tools-iuc,galaxyproject/tools-iuc,nekrut/tools-iuc,natefoo/tools-iuc,abretaud/tools-iuc,nsoranzo/tools-iuc,ieguinoa/tools-iuc,ieguinoa/tools-iuc,nsoranzo/tools-iuc,pavanvidem/tools-iuc,davebx/tools-iuc,jj-umn/tools-iuc,Delphine-L/tools-iuc,mvdbeek/tools-iuc,loraine-gueguen/tools-iuc,gregvonkuster/tools-iuc,gregvonkuster/tools-iuc,natefoo/tools-iuc,gregvonkuster/tools-iuc,Delphine-L/tools-iuc,galaxyproject/tools-iuc,loraine-gueguen/tools-iuc,jj-umn/tools-iuc,natefoo/tools-iuc,nekrut/tools-iuc,abretaud/tools-iuc,nekrut/tools-iuc,galaxyproject/tools-iuc,Delphine-L/tools-iuc,ieguinoa/tools-iuc,nsoranzo/tools-iuc,jj-umn/tools-iuc,jj-umn/tools-iuc,blankenberg/tools-iuc,jj-umn/tools-iuc,gregvonkuster/tools-iuc,ieguinoa/tools-iuc