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comparison samtools_sort.xml @ 0:4cafbe1d2ea6

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initial commit
author martenson <cech.marten@gmail.com>
date Wed, 10 Sep 2014 23:06:15 -0400
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615
616 <div class="blob-wrapper data type-xml">
617 <table class="highlight tab-size-8 js-file-line-container">
618 <tr>
619 <td id="L1" class="blob-num js-line-number" data-line-number="1"></td>
620 <td id="LC1" class="blob-code js-file-line"><span class="nt">&lt;tool</span> <span class="na">id=</span><span class="s">&quot;samtools_sort&quot;</span> <span class="na">name=</span><span class="s">&quot;sort&quot;</span> <span class="na">version=</span><span class="s">&quot;1.0.2&quot;</span><span class="nt">&gt;</span></td>
621 </tr>
622 <tr>
623 <td id="L2" class="blob-num js-line-number" data-line-number="2"></td>
624 <td id="LC2" class="blob-code js-file-line"> <span class="nt">&lt;requirements&gt;</span></td>
625 </tr>
626 <tr>
627 <td id="L3" class="blob-num js-line-number" data-line-number="3"></td>
628 <td id="LC3" class="blob-code js-file-line"> <span class="nt">&lt;requirement</span> <span class="na">type=</span><span class="s">&quot;package&quot;</span> <span class="na">version=</span><span class="s">&quot;0.1.19&quot;</span><span class="nt">&gt;</span>samtools<span class="nt">&lt;/requirement&gt;</span></td>
629 </tr>
630 <tr>
631 <td id="L4" class="blob-num js-line-number" data-line-number="4"></td>
632 <td id="LC4" class="blob-code js-file-line"> <span class="nt">&lt;/requirements&gt;</span></td>
633 </tr>
634 <tr>
635 <td id="L5" class="blob-num js-line-number" data-line-number="5"></td>
636 <td id="LC5" class="blob-code js-file-line"> <span class="nt">&lt;description&gt;</span>a BAM file<span class="nt">&lt;/description&gt;</span></td>
637 </tr>
638 <tr>
639 <td id="L6" class="blob-num js-line-number" data-line-number="6"></td>
640 <td id="LC6" class="blob-code js-file-line"> <span class="nt">&lt;command&gt;</span></td>
641 </tr>
642 <tr>
643 <td id="L7" class="blob-num js-line-number" data-line-number="7"></td>
644 <td id="LC7" class="blob-code js-file-line"> samtools sort</td>
645 </tr>
646 <tr>
647 <td id="L8" class="blob-num js-line-number" data-line-number="8"></td>
648 <td id="LC8" class="blob-code js-file-line"> $sort_mode</td>
649 </tr>
650 <tr>
651 <td id="L9" class="blob-num js-line-number" data-line-number="9"></td>
652 <td id="LC9" class="blob-code js-file-line"> &quot;${input1}&quot; foo</td>
653 </tr>
654 <tr>
655 <td id="L10" class="blob-num js-line-number" data-line-number="10"></td>
656 <td id="LC10" class="blob-code js-file-line"> 2<span class="ni">&amp;gt;&amp;amp;</span>1 || echo &quot;Error running samtools sort.&quot; <span class="ni">&amp;gt;&amp;amp;</span>2</td>
657 </tr>
658 <tr>
659 <td id="L11" class="blob-num js-line-number" data-line-number="11"></td>
660 <td id="LC11" class="blob-code js-file-line"> ;</td>
661 </tr>
662 <tr>
663 <td id="L12" class="blob-num js-line-number" data-line-number="12"></td>
664 <td id="LC12" class="blob-code js-file-line"> mv foo.bam &quot;${output1}&quot;</td>
665 </tr>
666 <tr>
667 <td id="L13" class="blob-num js-line-number" data-line-number="13"></td>
668 <td id="LC13" class="blob-code js-file-line"> <span class="nt">&lt;/command&gt;</span></td>
669 </tr>
670 <tr>
671 <td id="L14" class="blob-num js-line-number" data-line-number="14"></td>
672 <td id="LC14" class="blob-code js-file-line"> <span class="nt">&lt;inputs&gt;</span></td>
673 </tr>
674 <tr>
675 <td id="L15" class="blob-num js-line-number" data-line-number="15"></td>
676 <td id="LC15" class="blob-code js-file-line"> <span class="nt">&lt;param</span> <span class="na">name=</span><span class="s">&quot;input1&quot;</span> <span class="na">type=</span><span class="s">&quot;data&quot;</span> <span class="na">format=</span><span class="s">&quot;bam&quot;</span> <span class="na">label=</span><span class="s">&quot;BAM File&quot;</span> <span class="nt">/&gt;</span></td>
677 </tr>
678 <tr>
679 <td id="L16" class="blob-num js-line-number" data-line-number="16"></td>
680 <td id="LC16" class="blob-code js-file-line"> <span class="nt">&lt;param</span> <span class="na">name=</span><span class="s">&quot;sort_mode&quot;</span> <span class="na">type=</span><span class="s">&quot;select&quot;</span> <span class="na">label=</span><span class="s">&quot;Sort by &quot;</span><span class="nt">&gt;</span></td>
681 </tr>
682 <tr>
683 <td id="L17" class="blob-num js-line-number" data-line-number="17"></td>
684 <td id="LC17" class="blob-code js-file-line"> <span class="nt">&lt;option</span> <span class="na">value=</span><span class="s">&quot;&quot;</span> <span class="na">selected=</span><span class="s">&quot;True&quot;</span><span class="nt">&gt;</span>Chromosomal coordinates<span class="nt">&lt;/option&gt;</span></td>
685 </tr>
686 <tr>
687 <td id="L18" class="blob-num js-line-number" data-line-number="18"></td>
688 <td id="LC18" class="blob-code js-file-line"> <span class="nt">&lt;option</span> <span class="na">value=</span><span class="s">&quot;-n&quot;</span><span class="nt">&gt;</span>Read names<span class="nt">&lt;/option&gt;</span></td>
689 </tr>
690 <tr>
691 <td id="L19" class="blob-num js-line-number" data-line-number="19"></td>
692 <td id="LC19" class="blob-code js-file-line"> <span class="nt">&lt;/param&gt;</span></td>
693 </tr>
694 <tr>
695 <td id="L20" class="blob-num js-line-number" data-line-number="20"></td>
696 <td id="LC20" class="blob-code js-file-line"> <span class="nt">&lt;/inputs&gt;</span></td>
697 </tr>
698 <tr>
699 <td id="L21" class="blob-num js-line-number" data-line-number="21"></td>
700 <td id="LC21" class="blob-code js-file-line"> <span class="nt">&lt;outputs&gt;</span></td>
701 </tr>
702 <tr>
703 <td id="L22" class="blob-num js-line-number" data-line-number="22"></td>
704 <td id="LC22" class="blob-code js-file-line"> <span class="nt">&lt;data</span> <span class="na">name=</span><span class="s">&quot;output1&quot;</span> <span class="na">format=</span><span class="s">&quot;bam&quot;</span> <span class="nt">/&gt;</span></td>
705 </tr>
706 <tr>
707 <td id="L23" class="blob-num js-line-number" data-line-number="23"></td>
708 <td id="LC23" class="blob-code js-file-line"> <span class="nt">&lt;/outputs&gt;</span></td>
709 </tr>
710 <tr>
711 <td id="L24" class="blob-num js-line-number" data-line-number="24"></td>
712 <td id="LC24" class="blob-code js-file-line"> <span class="nt">&lt;tests&gt;</span></td>
713 </tr>
714 <tr>
715 <td id="L25" class="blob-num js-line-number" data-line-number="25"></td>
716 <td id="LC25" class="blob-code js-file-line"> <span class="nt">&lt;test&gt;</span></td>
717 </tr>
718 <tr>
719 <td id="L26" class="blob-num js-line-number" data-line-number="26"></td>
720 <td id="LC26" class="blob-code js-file-line"> <span class="nt">&lt;param</span> <span class="na">name=</span><span class="s">&quot;input1&quot;</span> <span class="na">value=</span><span class="s">&quot;1.bam&quot;</span> <span class="na">ftype=</span><span class="s">&quot;bam&quot;</span> <span class="nt">/&gt;</span></td>
721 </tr>
722 <tr>
723 <td id="L27" class="blob-num js-line-number" data-line-number="27"></td>
724 <td id="LC27" class="blob-code js-file-line"> <span class="nt">&lt;output</span> <span class="na">name=</span><span class="s">&quot;output1&quot;</span> <span class="na">file=</span><span class="s">&quot;1_sort.bam&quot;</span> <span class="na">ftype=</span><span class="s">&quot;bam&quot;</span> <span class="na">sort=</span><span class="s">&quot;True&quot;</span><span class="nt">/&gt;</span></td>
725 </tr>
726 <tr>
727 <td id="L28" class="blob-num js-line-number" data-line-number="28"></td>
728 <td id="LC28" class="blob-code js-file-line"> <span class="nt">&lt;/test&gt;</span></td>
729 </tr>
730 <tr>
731 <td id="L29" class="blob-num js-line-number" data-line-number="29"></td>
732 <td id="LC29" class="blob-code js-file-line"> <span class="nt">&lt;/tests&gt;</span></td>
733 </tr>
734 <tr>
735 <td id="L30" class="blob-num js-line-number" data-line-number="30"></td>
736 <td id="LC30" class="blob-code js-file-line"> <span class="nt">&lt;help&gt;</span></td>
737 </tr>
738 <tr>
739 <td id="L31" class="blob-num js-line-number" data-line-number="31"></td>
740 <td id="LC31" class="blob-code js-file-line">
741 </td>
742 </tr>
743 <tr>
744 <td id="L32" class="blob-num js-line-number" data-line-number="32"></td>
745 <td id="LC32" class="blob-code js-file-line">**What it does**</td>
746 </tr>
747 <tr>
748 <td id="L33" class="blob-num js-line-number" data-line-number="33"></td>
749 <td id="LC33" class="blob-code js-file-line">
750 </td>
751 </tr>
752 <tr>
753 <td id="L34" class="blob-num js-line-number" data-line-number="34"></td>
754 <td id="LC34" class="blob-code js-file-line">This tool uses the SAMTools_ toolkit to sort alignments by leftmost coordinates or read names.</td>
755 </tr>
756 <tr>
757 <td id="L35" class="blob-num js-line-number" data-line-number="35"></td>
758 <td id="LC35" class="blob-code js-file-line">
759 </td>
760 </tr>
761 <tr>
762 <td id="L36" class="blob-num js-line-number" data-line-number="36"></td>
763 <td id="LC36" class="blob-code js-file-line">.. _SAMTools: http://samtools.sourceforge.net/samtools.shtml</td>
764 </tr>
765 <tr>
766 <td id="L37" class="blob-num js-line-number" data-line-number="37"></td>
767 <td id="LC37" class="blob-code js-file-line">
768 </td>
769 </tr>
770 <tr>
771 <td id="L38" class="blob-num js-line-number" data-line-number="38"></td>
772 <td id="LC38" class="blob-code js-file-line">------</td>
773 </tr>
774 <tr>
775 <td id="L39" class="blob-num js-line-number" data-line-number="39"></td>
776 <td id="LC39" class="blob-code js-file-line">
777 </td>
778 </tr>
779 <tr>
780 <td id="L40" class="blob-num js-line-number" data-line-number="40"></td>
781 <td id="LC40" class="blob-code js-file-line">**Citation**</td>
782 </tr>
783 <tr>
784 <td id="L41" class="blob-num js-line-number" data-line-number="41"></td>
785 <td id="LC41" class="blob-code js-file-line">
786 </td>
787 </tr>
788 <tr>
789 <td id="L42" class="blob-num js-line-number" data-line-number="42"></td>
790 <td id="LC42" class="blob-code js-file-line">For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. <span class="ni">&amp;lt;</span>http://www.ncbi.nlm.nih.gov/pubmed/19505943<span class="ni">&amp;gt;</span>`_</td>
791 </tr>
792 <tr>
793 <td id="L43" class="blob-num js-line-number" data-line-number="43"></td>
794 <td id="LC43" class="blob-code js-file-line">
795 </td>
796 </tr>
797 <tr>
798 <td id="L44" class="blob-num js-line-number" data-line-number="44"></td>
799 <td id="LC44" class="blob-code js-file-line">If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*</td>
800 </tr>
801 <tr>
802 <td id="L45" class="blob-num js-line-number" data-line-number="45"></td>
803 <td id="LC45" class="blob-code js-file-line">
804 </td>
805 </tr>
806 <tr>
807 <td id="L46" class="blob-num js-line-number" data-line-number="46"></td>
808 <td id="LC46" class="blob-code js-file-line"> <span class="nt">&lt;/help&gt;</span></td>
809 </tr>
810 <tr>
811 <td id="L47" class="blob-num js-line-number" data-line-number="47"></td>
812 <td id="LC47" class="blob-code js-file-line"><span class="nt">&lt;/tool&gt;</span></td>
813 </tr>
814 </table>
815
816 </div>
817
818 </div>
819 </div>
820
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