--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/get_data/cfg/getcfgcells.xml	Wed Mar 23 14:35:56 2016 -0400
@@ -0,0 +1,324 @@
+<tool id="glytools_get_CFG_cell" name="GAP Get CFG cell" version="0.3">
+
+    <description>download msa entries from CFG</description>
+    <requirements>
+        <requirement type="package" version="1.0">python_for_glycan_tools</requirement>
+    </requirements>
+<stdio>
+    <regex match="IOError" 
+           source="both" 
+           level="fatal" 
+           description="IOError" />
+    <regex match="UserWarning: gzip transfer encoding is experimental" 
+           source="both" 
+           level="warning" 
+           description="Warning re use of gzip encoding" />
+    <regex match="br.set_handle_gzip(True)" 
+           source="both" 
+           level="warning" 
+           description="Warning re use of gzip encoding" />
+    <regex match="IOError" 
+           source="both" 
+           level="fatal" 
+           description="IOError" />
+</stdio>
+    <command interpreter="python"><![CDATA[ cfg_get_glycan_from_cells.py -s "$species" -p "$investigator" -g "$glycantype" -c "$celltype" -o "$html_file" --filepath "msa_output" ]]></command>
+    <inputs>
+        <param name="species" type="select" label="Species">
+            <option value="Chinese Hamster" selected="false">Chinese Hamster</option>
+            <option value="Human" selected="true">Human</option>
+            <option value="Mouse" selected="false">Mouse</option>
+            <option value="all" selected="false">all</option>
+        </param>
+        <param name="investigator" type="select" label="Investigator">
+            <option value="all" selected="true">all</option>
+            <option value="Agbandje-McKenna, Mavis" selected="false">
+                Agbandje-McKenna, Mavis
+            </option>
+            <option value="Appelmelk, Ben J. " selected="false">
+                Appelmelk, Ben J.
+            </option>
+            <option value="Bennett, Eric" selected="false">
+                Bennett, Eric
+            </option>
+            <option value="Bochner, Bruce S." selected="false">
+                Bochner, Bruce S.
+            </option>
+            <option value="Cheng, Pi-Wan" selected="false">
+                Cheng, Pi-Wan
+            </option>
+            <option value="Contag, Christopher" selected="false">
+                Contag, Christopher
+            </option>
+            <option value="Cook-Mills, Joan" selected="false">
+                Cook-Mills, Joan
+            </option>
+            <option value="Crocker,Paul" selected="false">
+                Crocker,Paul
+            </option>
+            <option value="Cummings,Richard D. " selected="false">
+                Cummings,Richard D.
+            </option>
+            <option value="Dennis, James W." selected="false">
+                Dennis, James W.
+            </option>
+            <option value="Dimitroff, Charles" selected="false">
+                Dimitroff, Charles
+            </option>
+            <option value="Gordon, Siamon" selected="false">
+                Gordon, Siamon
+            </option>
+            <option value="Henion, Timothy" selected="false">
+                Henion, Timothy
+            </option>
+            <option value="Jackson, David " selected="false">
+                Jackson, David
+            </option>
+            <option value="Jaye, David" selected="false">
+                Jaye, David
+            </option>
+            <option value="Liu, FuTong" selected="false">
+                Liu, FuTong
+            </option>
+            <option value="Mahal, Lara K." selected="false">
+                Mahal, Lara K.
+            </option>
+            <option value="Merrill, Alfred" selected="false">
+                Merrill, Alfred
+            </option>
+            <option value="Metcalfe, Dean D." selected="false">
+                Metcalfe, Dean D.
+            </option>
+            <option value="Nitschke, Lars" selected="false">
+                Nitschke, Lars
+            </option>
+            <option value="Panjwani, Noorjahan" selected="false">
+                Panjwani, Noorjahan
+            </option>
+            <option value="Paulson, Henry" selected="false">
+                Paulson, Henry
+            </option>
+            <option value="Paulson, James" selected="false">
+                Paulson, James
+            </option>
+            <option value="Rittenhouse-Olson, Kate" selected="false">
+                Rittenhouse-Olson, Kate
+            </option>
+            <option value="Romagne, Francois" selected="false">
+                Romagne, Francois
+            </option>
+            <option value="Salomon,Daniel " selected="false">
+                Salomon,Daniel
+            </option>
+            <option value="Stanley, Pamela" selected="false">
+                Stanley, Pamela
+            </option>
+            <option value="Van Kooyk, Yvette" selected="false">
+                Van Kooyk, Yvette
+            </option>
+            <option value="Wild, Martin K." selected="false">
+                Wild, Martin K.
+            </option>
+            <option value="Wu, Hui" selected="false">
+                Wu, Hui
+            </option>
+        </param>
+        <param name="glycantype" type="select" label="Glycan Type Analysed">
+            <option value="all" selected="true">all</option>
+            <option value="N-Linked" selected="false">
+                N-Linked
+            </option>
+            <option value="Non-Polar Glycolipids" selected="false">
+                Non-Polar Glycolipids
+            </option>
+            <option value="O-Linked" selected="false">
+                O-Linked
+            </option>
+            <option value="Polar Glycolipids" selected="false">
+                Polar Glycolipids
+            </option>
+        </param>
+        <param name="celltype" type="select" label="Cell Type">
+            <option value="all" selected="true">all</option>
+            <option value="A9 fibroblasts" selected="false">
+                A9 fibroblasts
+            </option>
+            <option value="Antibodies" selected="false">
+                Antibodies
+            </option>
+            <option value="B-Cells" selected="false">
+                B-Cells
+            </option>
+            <option value="B1 Cells" selected="false">
+                B1 Cells
+            </option>
+            <option value="Basophils" selected="false">
+                Basophils
+            </option>
+            <option value="Bone marrow mast cells (BMMC)" selected="false">
+                Bone marrow mast cells (BMMC)
+            </option>
+            <option value="CHO" selected="false">
+                CHO
+            </option>
+            <option value="CHO  -Lec10.3C" selected="false">
+                CHO -Lec10.3C
+            </option>
+            <option value="CHO -Lec1.3C" selected="false">
+                CHO -Lec1.3C
+            </option>
+            <option value="CHO -Lec13.6A" selected="false">
+                CHO -Lec13.6A
+            </option>
+            <option value="CHO -Lec2.6A" selected="false">
+                CHO -Lec2.6A
+            </option>
+            <option value="CHO -Lec4.7B" selected="false">
+                CHO -Lec4.7B
+            </option>
+            <option value="CHO LEC11.E7" selected="false">
+                CHO LEC11.E7
+            </option>
+            <option value="CHO LEC12.1B" selected="false">
+                CHO LEC12.1B
+            </option>
+            <option value="CHO LEC14.4A" selected="false">
+                CHO LEC14.4A
+            </option>
+            <option value="CHO LEC18.21B" selected="false">
+                CHO LEC18.21B
+            </option>
+            <option value="CHO LEC30.H2" selected="false">
+                CHO LEC30.H2
+            </option>
+            <option value="Cytokine-induced killer (CIK) cells" selected="false">
+                Cytokine-induced killer (CIK) cells
+            </option>
+            <option value="Dendritic Cells" selected="false">
+                Dendritic Cells
+            </option>
+            <option value="EL4 T lymphocytes" selected="false">
+                EL4 T lymphocytes
+            </option>
+            <option value="Eosinophils " selected="false">
+                Eosinophils
+            </option>
+            <option value="Erythrocytes" selected="false">
+                Erythrocytes
+            </option>
+            <option value="HL-60" selected="false">
+                HL-60
+            </option>
+            <option value="HeLa EV2" selected="false">
+                HeLa EV2
+            </option>
+            <option value="HeLa PF" selected="false">
+                HeLa PF
+            </option>
+            <option value="Human Dermal Lymphatic Endothelial Cells (HDLEC) " selected="false">
+                Human Dermal Lymphatic Endothelial Cells (HDLEC)
+            </option>
+            <option value="Human Prostate LNCaP Cells " selected="false">
+                Human Prostate LNCaP Cells
+            </option>
+            <option value="Immunoglobulin (Plasma extract) " selected="false">
+                Immunoglobulin (Plasma extract)
+            </option>
+            <option value="K562" selected="false">
+                K562
+            </option>
+            <option value="KG-1a" selected="false">
+                KG-1a
+            </option>
+            <option value="KG1a Cells" selected="false">
+                KG1a Cells
+            </option>
+            <option value="Macrophages" selected="false">
+                Macrophages
+            </option>
+            <option value="Mast Cells" selected="false">
+                Mast Cells
+            </option>
+            <option value="Monocytes" selected="false">
+                Monocytes
+            </option>
+            <option value="Murine mammary carcinoma" selected="false">
+                Murine mammary carcinoma
+            </option>
+            <option value="Natural Killer Cells" selected="false">
+                Natural Killer Cells
+            </option>
+            <option value="Natural killer cells" selected="false">
+                Natural killer cells
+            </option>
+            <option value="Neurons" selected="false">
+                Neurons
+            </option>
+            <option value="Neutrophils" selected="false">
+                Neutrophils
+            </option>
+            <option value="Osteoclasts" selected="false">
+                Osteoclasts
+            </option>
+            <option value="Peripheral Blood Mononuclear Cells (PBMC)" selected="false">
+                Peripheral Blood Mononuclear Cells (PBMC)
+            </option>
+            <option value="RAW" selected="false">
+                RAW
+            </option>
+            <option value="RAW 264.7 Cells" selected="false">
+                RAW 264.7 Cells
+            </option>
+            <option value="SV40 transformed fibroblast cell line, NB324K" selected="false">
+                SV40 transformed fibroblast cell line, NB324K
+            </option>
+            <option value="T-Cells" selected="false">
+                T-Cells
+            </option>
+            <option value="THP-1" selected="false">
+                THP-1
+            </option>
+            <option value="VG37" selected="false">
+                VG37
+            </option>
+            <option value="WEHI 231 B Cells" selected="false">
+                WEHI 231 B Cells
+            </option>
+            <option value="WEHI-3" selected="false">
+                WEHI-3
+            </option>
+        </param>
+    </inputs>
+        <outputs>
+        <data format="html" name="html_file" label="Summary_${tool.name}.html">
+	<discover_datasets pattern="__designation_and_ext__" directory="msa_output" visible="true" />
+	        </data>
+	</outputs>
+    <help> <![CDATA[ 
+.. class:: infomark
+
+**What this tool does**
+
+This tool will request Annotated Mass spec (msa) data from the Consortium for Functional Glycomics. 
+
+.. class:: infomark
+
+**Input**
+
+Your choice of Species, Participating Investigator, Glycan type and Cell type as per the CFG request page.
+
+----
+
+.. class:: infomark
+
+**Output**
+
+HTML summary of retrieved information (Note links in html do not function within Galaxy).
+
+A number of autodiscovered msa datasets (refresh browser if necessary).
+
+
+]]>
+    </help>
+
+</tool>