I have modified the shed tool conf xml in order to add labels to tool sections and it appears to now be reading the xml in reverse and ordering the tools in the tool panel incorrectly. Image of issue: https://www.dropbox.com/s/rxbr2tpqkpeeysw/Screen%20Shot%202016-10-12%20at%20... ~~~~ <?xml version="1.0"?> <toolbox tool_path="../shed_tools"> <section id="hts:_rna_analysis" name="HTS: RNA Analysis" version=""> <label id="mapping" text="Mapping" /> <tool file="toolshed.g2.bx.psu.edu/repos/devteam/tophat2/758594ed0364/tophat2/tophat2_wrapper.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/2.1.0"> <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> <repository_name>tophat2</repository_name> <repository_owner>devteam</repository_owner> <installed_changeset_revision>758594ed0364</installed_changeset_revision> <id>toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/2.1.0</id> <version>2.1.0</version> </tool> <tool file="toolshed.g2.bx.psu.edu/repos/iuc/hisat2/1eb21dccc2fa/hisat2/hisat2.xml" guid="toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.0.3"> <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> <repository_name>hisat2</repository_name> <repository_owner>iuc</repository_owner> <installed_changeset_revision>1eb21dccc2fa</installed_changeset_revision> <id>toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.0.3</id> <version>2.0.3</version> </tool> <tool file="toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/ace9f5a2b40f/rgrnastar/rg_rnaStar.xml" guid="toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.4.0d-2"> <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> <repository_name>rgrnastar</repository_name> <repository_owner>iuc</repository_owner> <installed_changeset_revision>ace9f5a2b40f</installed_changeset_revision> <id>toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.4.0d-2</id> <version>2.4.0d-2</version> </tool> <label id="cuf_lnks" text="Cufflinks" /> <tool file="toolshed.g2.bx.psu.edu/repos/devteam/cuffcompare/b77178f66fc3/cuffcompare/cuffcompare_wrapper.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/cuffcompare/cuffcompare/2.2.1.0"> <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> <repository_name>cuffcompare</repository_name> <repository_owner>devteam</repository_owner> <installed_changeset_revision>b77178f66fc3</installed_changeset_revision> <id>toolshed.g2.bx.psu.edu/repos/devteam/cuffcompare/cuffcompare/2.2.1.0</id> <version>2.2.1.0</version> </tool> <tool file="toolshed.g2.bx.psu.edu/repos/devteam/cuffquant/986b63735a5e/cuffquant/cuffquant_wrapper.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/cuffquant/cuffquant/2.2.1.0"> <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> <repository_name>cuffquant</repository_name> <repository_owner>devteam</repository_owner> <installed_changeset_revision>986b63735a5e</installed_changeset_revision> <id>toolshed.g2.bx.psu.edu/repos/devteam/cuffquant/cuffquant/2.2.1.0</id> <version>2.2.1.0</version> </tool> <tool file="toolshed.g2.bx.psu.edu/repos/devteam/cuffmerge/8160c8ea4eb9/cuffmerge/cuffmerge_wrapper.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/cuffmerge/cuffmerge/2.2.1.0"> <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> <repository_name>cuffmerge</repository_name> <repository_owner>devteam</repository_owner> <installed_changeset_revision>8160c8ea4eb9</installed_changeset_revision> <id>toolshed.g2.bx.psu.edu/repos/devteam/cuffmerge/cuffmerge/2.2.1.0</id> <version>2.2.1.0</version> </tool> <tool file="toolshed.g2.bx.psu.edu/repos/devteam/cuffnorm/a26af05ac218/cuffnorm/cuffnorm_wrapper.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/cuffnorm/cuffnorm/2.2.1.0"> <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> <repository_name>cuffnorm</repository_name> <repository_owner>devteam</repository_owner> <installed_changeset_revision>a26af05ac218</installed_changeset_revision> <id>toolshed.g2.bx.psu.edu/repos/devteam/cuffnorm/cuffnorm/2.2.1.0</id> <version>2.2.1.0</version> </tool> <tool file="toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/9aab29e159a7/cufflinks/cufflinks_wrapper.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/0.0.7"> <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> <repository_name>cufflinks</repository_name> <repository_owner>devteam</repository_owner> <installed_changeset_revision>9aab29e159a7</installed_changeset_revision> <id>toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/0.0.7</id> <version>0.0.7</version> </tool> <tool file="toolshed.g2.bx.psu.edu/repos/devteam/cuffdiff/0f32ad418df8/cuffdiff/cuffdiff_wrapper.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/cuffdiff/cuffdiff/2.2.1.3"> <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> <repository_name>cuffdiff</repository_name> <repository_owner>devteam</repository_owner> <installed_changeset_revision>0f32ad418df8</installed_changeset_revision> <id>toolshed.g2.bx.psu.edu/repos/devteam/cuffdiff/cuffdiff/2.2.1.3</id> <version>2.2.1.3</version> </tool> <tool file="toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/a1ea9af8d5f4/cufflinks/cufflinks_wrapper.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.0"> <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> <repository_name>cufflinks</repository_name> <repository_owner>devteam</repository_owner> <installed_changeset_revision>a1ea9af8d5f4</installed_changeset_revision> <id>toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.0</id> <version>2.2.1.0</version> </tool> <tool file="toolshed.g2.bx.psu.edu/repos/devteam/cuffnorm/7d4c2097aac5/cuffnorm/cuffnorm_wrapper.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/cuffnorm/cuffnorm/2.2.1.1"> <tool_shed>toolshed.g2.bx.psu.edu</tool_shed> <repository_name>cuffnorm</repository_name> <repository_owner>devteam</repository_owner> <installed_changeset_revision>7d4c2097aac5</installed_changeset_revision> <id>toolshed.g2.bx.psu.edu/repos/devteam/cuffnorm/cuffnorm/2.2.1.1</id> <version>2.2.1.1</version> </tool> </section> ~~~~